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Identification of CRF89_BF, a new member of an HIV-1 circulating BF intersubtype recombinant form family widely spread in South America. Sci Rep 2021; 11:11442. [PMID: 34075073 PMCID: PMC8169922 DOI: 10.1038/s41598-021-90023-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 04/28/2021] [Indexed: 01/10/2023] Open
Abstract
Circulating recombinant forms (CRFs) contribute substantially to the HIV-1 pandemic. Among 105 CRFs described in the literature, 16 are BF intersubtype recombinants, most of South American origin, of which CRF12_BF is the most widely spread. A BF recombinant cluster identified in Bolivia was suggested to represent a new CRF_BF. Here we find that it belongs to a larger cluster incorporating 39 viruses collected in 7 countries from 3 continents, 22 of them in Spain, most from Bolivian or Peruvian individuals, and 12 in South America (Bolivia, Argentina, and Peru). This BF cluster comprises three major subclusters, two associated with Bolivian and one with Peruvian individuals. Near full-length genome sequence analyses of nine viruses, collected in Spain, Bolivia, and Peru, revealed coincident BF mosaic structures, with 13 breakpoints, 6 and 7 of which coincided with CRF12_BF and CRF17_BF, respectively. In a phylogenetic tree, they grouped in a clade closely related to these CRFs, and more distantly to CRF38_BF and CRF44_BF, all circulating in South America. These results allowed to identify a new HIV-1 CRF, designated CRF89_BF. Through phylodynamic analyses, CRF89_BF emergence was estimated in Bolivia around 1986. CRF89_BF is the fifth CRF member of the HIV-1 recombinant family related to CRF12_BF.
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Gibson KM, Steiner MC, Rentia U, Bendall ML, Pérez-Losada M, Crandall KA. Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses. Viruses 2020; 12:E758. [PMID: 32674515 PMCID: PMC7412389 DOI: 10.3390/v12070758] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 01/04/2023] Open
Abstract
Next-generation sequencing (NGS) offers a powerful opportunity to identify low-abundance, intra-host viral sequence variants, yet the focus of many bioinformatic tools on consensus sequence construction has precluded a thorough analysis of intra-host diversity. To take full advantage of the resolution of NGS data, we developed HAplotype PHylodynamics PIPEline (HAPHPIPE), an open-source tool for the de novo and reference-based assembly of viral NGS data, with both consensus sequence assembly and a focus on the quantification of intra-host variation through haplotype reconstruction. We validate and compare the consensus sequence assembly methods of HAPHPIPE to those of two alternative software packages, HyDRA and Geneious, using simulated HIV and empirical HIV, HCV, and SARS-CoV-2 datasets. Our validation methods included read mapping, genetic distance, and genetic diversity metrics. In simulated NGS data, HAPHPIPE generated pol consensus sequences significantly closer to the true consensus sequence than those produced by HyDRA and Geneious and performed comparably to Geneious for HIV gp120 sequences. Furthermore, using empirical data from multiple viruses, we demonstrate that HAPHPIPE can analyze larger sequence datasets due to its greater computational speed. Therefore, we contend that HAPHPIPE provides a more user-friendly platform for users with and without bioinformatics experience to implement current best practices for viral NGS assembly than other currently available options.
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Affiliation(s)
- Keylie M. Gibson
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
| | - Margaret C. Steiner
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
| | - Uzma Rentia
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
| | - Matthew L. Bendall
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
| | - Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4169-007 Vairão, Portugal
| | - Keith A. Crandall
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA
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HIV-1 genetic diversity and demographic characteristics in Bulgaria. PLoS One 2019; 14:e0217063. [PMID: 31136611 PMCID: PMC6538145 DOI: 10.1371/journal.pone.0217063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 05/03/2019] [Indexed: 12/14/2022] Open
Abstract
HIV-1 strain diversity in Bulgaria is extensive and includes contributions from nearly all major subtypes and the Circulating Recombinant Forms (CRF): 01_AE, 02_AG, and 05_DF. Prior to this study, HIV-1 sequence information from Bulgaria has been based solely on the pro-RT gene, which represent less than 15% of the viral genome. To further characterize HIV-1 in Bulgaria, assess participant risk behaviors, and strengthen knowledge of circulating strains in the region, the study “Genetic Subtypes of HIV-1 in Bulgaria (RV240)” was conducted. This study employed the real time-PCR based Multi-region Hybridization Assay (MHA) B/non-B and HIV-1 sequencing to survey 215 of the approximately 1100 known HIV-1 infected Bulgarian adults (2008–2009) and determine if they were infected with subtype B HIV-1. The results indicated a subtype B prevalence of 40% and demonstrate the application of the MHA B/non-B in an area containing broad HIV-1 strain diversity. Within the assessed risk behaviors, the proportion of subtype B infection was greatest in men who have sex with men and lowest among those with drug use risk factors. During this study, 15 near full-length genomes and 22 envelope sequences were isolated from study participants. Phylogenetic analysis shows the presence of subtypes A1, B, C, F1, and G, CRF01_AE, CRF02_AG, CRF05_DF, and one unique recombinant form (URF). These sequences also show the presence of two strain groups containing participants with similar risk factors. Previous studies in African and Asian cohorts have shown that co-circulation of multiple subtypes can lead to viral recombination within super-infected individuals and the emergence of new URFs. The low prevalence of URFs in the presence of high subtype diversity in this study, may be the result of successful infection prevention and control programs. Continued epidemiological monitoring and support of infection prevention programs will help maintain control of the HIV-1 epidemic in Bulgaria.
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Hernandez I, Reina-Ortiz M, K. Yusuf K, Ochoa T, Rosas C, Sharma V, Naik E, Salihu HM, Terán S, Izurieta R, Teran E. Risk factors for HIV and STI among female sex workers in a high HIV prevalent region of Ecuador. COGENT MEDICINE 2019. [DOI: 10.1080/2331205x.2019.1565292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Isabel Hernandez
- Facultad de Enfermería, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Colegio de Ciencias de la Salud, Universidad San Francisco de Quito, Quito, Ecuador
| | - Miguel Reina-Ortiz
- Department of Global Health, College of Public Health, University of South Florida, Tampa, FL, USA
- Fundación Raíces, Esmeraldas, Ecuador
| | - Korede K. Yusuf
- Department of Global Health, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Tatiana Ochoa
- Department of Global Health, College of Public Health, University of South Florida, Tampa, FL, USA
- Moffitt Cancer Center, Tampa, FL, USA
| | - Carlos Rosas
- Colegio de Ciencias de la Salud, Universidad San Francisco de Quito, Quito, Ecuador
| | - Vinita Sharma
- Colegio de Ciencias de la Salud, Universidad San Francisco de Quito, Quito, Ecuador
| | - Eknath Naik
- Department of Global Health, College of Public Health, University of South Florida, Tampa, FL, USA
| | | | - Santiago Terán
- Colegio de Ciencias de la Salud, Universidad San Francisco de Quito, Quito, Ecuador
| | - Ricardo Izurieta
- Colegio de Ciencias de la Salud, Universidad San Francisco de Quito, Quito, Ecuador
| | - Enrique Teran
- Colegio de Ciencias de la Salud, Universidad San Francisco de Quito, Quito, Ecuador
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Hahn F, Schmalen A, Setz C, Friedrich M, Schlößer S, Kölle J, Spranger R, Rauch P, Fraedrich K, Reif T, Karius-Fischer J, Balasubramanyam A, Henklein P, Fossen T, Schubert U. Proteolysis of mature HIV-1 p6 Gag protein by the insulin-degrading enzyme (IDE) regulates virus replication in an Env-dependent manner. PLoS One 2017; 12:e0174254. [PMID: 28388673 PMCID: PMC5384750 DOI: 10.1371/journal.pone.0174254] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 03/06/2017] [Indexed: 12/18/2022] Open
Abstract
There is a significantly higher risk for type II diabetes in HIV-1 carriers, albeit the molecular mechanism for this HIV-related pathology remains enigmatic. The 52 amino acid HIV-1 p6 Gag protein is synthesized as the C-terminal part of the Gag polyprotein Pr55. In this context, p6 promotes virus release by its two late (L-) domains, and facilitates the incorporation of the viral accessory protein Vpr. However, the function of p6 in its mature form, after proteolytic release from Gag, has not been investigated yet. We found that the mature p6 represents the first known viral substrate of the ubiquitously expressed cytosolic metalloendopeptidase insulin-degrading enzyme (IDE). IDE is sufficient and required for degradation of p6, and p6 is approximately 100-fold more efficiently degraded by IDE than its eponymous substrate insulin. This observation appears to be specific for HIV-1, as p6 proteins from HIV-2 and simian immunodeficiency virus, as well as the 51 amino acid p9 from equine infectious anaemia virus were insensitive to IDE degradation. The amount of virus-associated p6, as well as the efficiency of release and maturation of progeny viruses does not depend on the presence of IDE in the host cells, as it was shown by CRISPR/Cas9 edited IDE KO cells. However, HIV-1 mutants harboring IDE-insensitive p6 variants exhibit reduced virus replication capacity, a phenomenon that seems to depend on the presence of an X4-tropic Env. Furthermore, competing for IDE by exogenous insulin or inhibiting IDE by the highly specific inhibitor 6bK, also reduced virus replication. This effect could be specifically attributed to IDE since replication of HIV-1 variants coding for an IDE-insensitive p6 were inert towards IDE-inhibition. Our cumulative data support a model in which removal of p6 during viral entry is important for virus replication, at least in the case of X4 tropic HIV-1.
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Affiliation(s)
- Friedrich Hahn
- Institute of Virology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Adrian Schmalen
- Institute of Virology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Christian Setz
- Institute of Virology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Melanie Friedrich
- Institute of Virology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Stefan Schlößer
- Institute of Virology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Julia Kölle
- Institute of Virology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Robert Spranger
- Institute of Virology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Pia Rauch
- Institute of Virology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Kirsten Fraedrich
- Institute of Virology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Tatjana Reif
- Institute of Virology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Julia Karius-Fischer
- Institute of Virology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Ashok Balasubramanyam
- Translational Metabolism Unit, Diabetes Research Center, Division of Diabetes, Endocrinology and Metabolism, Baylor College of Medicine, Houston, Texas, United States of America
| | - Petra Henklein
- Institute of Biochemistry, Charité Universitätsmedizin-Berlin, Berlin, Germany
| | - Torgils Fossen
- Department of Chemistry and Centre for Pharmacy, University of Bergen, Bergen, Norway
| | - Ulrich Schubert
- Institute of Virology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
- * E-mail:
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Heipertz RA, Ayemoba O, Sanders-Buell E, Poltavee K, Pham P, Kijak GH, Lei E, Bose M, Howell S, O'Sullivan AM, Bates A, Cervenka T, Kuroiwa J, Akintunde A, Ibezim O, Alabi A, Okoye O, Manak M, Malia J, Peel S, Maisaka M, Singer D, O’Connell RJ, Robb ML, Kim JH, Michael NL, Njoku O, Tovanabutra S. Significant contribution of subtype G to HIV-1 genetic complexity in Nigeria identified by a newly developed subtyping assay specific for subtype G and CRF02_AG. Medicine (Baltimore) 2016; 95:e4346. [PMID: 27512845 PMCID: PMC4985300 DOI: 10.1097/md.0000000000004346] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
While abundant sequence information is available from human immunodeficiency virus type 1 (HIV-1) subtypes A, B, C and CRF01_AE for HIV-1 vaccine design, sequences from West Africa are less represented. We sought to augment our understanding of HIV-1 variants circulating in 6 Nigerian cities as a step to subsequent HIV-1 vaccine development.The G/CRF02_AG multi-region hybridization assay (MHA) was developed to differentiate subtype G, CRF02_AG and their recombinants from other subtypes based on 7 HIV-1 segments. Plasma from 224 HIV-1 infected volunteers enrolled in a cohort examining HIV-1 prevalence, risk factor, and subtype from Makurdi (30), Abuja (18), Enugu (11), Kaduna (12), Tafa (95), and Ojo/Lagos (58) was analyzed using MHA. HIV-1 genomes from 42 samples were sequenced to validate the MHA and fully explore the recombinant structure of G and CRF02_AG variants.The sensitivity and specificity of MHA varied between 73-100% and 90-100%, respectively. The subtype distribution as identified by MHA among 224 samples revealed 38% CRF02_AG, 28% G, and 26% G/CRF02_AG recombinants while 8% remained nontypeable strains. In envelope (env) gp120, 38.84% of the samples reacted to a G probe while 31.25% reacted to a CRF02 (subtype A) probe. Full genome characterization of 42 sequences revealed the complexity of Nigerian HIV-1 variants.CRF02_AG, subtype G, and their recombinants were the major circulating HIV-1 variants in 6 Nigerian cities. High proportions of samples reacted to a G probe in env gp120 confirms that subtype G infections are abundant and should be considered in strategies for global HIV-1 vaccine development.
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Affiliation(s)
- Richard A. Heipertz
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Ojor Ayemoba
- Emergency Plan Implementation Committee, Nigerian Ministry of Defense, Abuja, Nigeria
| | - Eric Sanders-Buell
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Kultida Poltavee
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Phuc Pham
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Gustavo H. Kijak
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Esther Lei
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Meera Bose
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Shana Howell
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Anne Marie O'Sullivan
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Adam Bates
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Taylor Cervenka
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Janelle Kuroiwa
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | | | - Onyekachukwu Ibezim
- Emergency Plan Implementation Committee, Nigerian Ministry of Defense, Abuja, Nigeria
| | - Abraham Alabi
- US Military HIV Research Program (HJF-MRI), Abuja, Nigeria
- Centre de Recherches Medicales de Lambarene (CERMEL) Fondation Internationale de l’Hôpital Albert Schweitzer Lambarene, Gabon
| | - Obumneke Okoye
- Emergency Plan Implementation Committee, Nigerian Ministry of Defense, Abuja, Nigeria
| | - Mark Manak
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Jennifer Malia
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- United States Public Health Service, Rockville, Maryland
| | - Sheila Peel
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | - Darrell Singer
- United States Public Health Service, Rockville, Maryland
- Department of Defense HIV Program, Abuja, Nigeria
| | - Robert J. O’Connell
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Merlin L. Robb
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Jerome H. Kim
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Nelson L. Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | - Sodsai Tovanabutra
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
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Lu X, Kang X, Chen S, Zhao H, Liu Y, Zhao C, Zhang Y, Li J, Cui Z, Wang X. HIV-1 Genetic Diversity and Transmitted Drug Resistance Among Recently Infected Individuals at Men Who Have Sex with Men Sentinel Surveillance Points in Hebei Province, China. AIDS Res Hum Retroviruses 2015. [PMID: 26200883 DOI: 10.1089/aid.2015.0160] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
For this study, 50 HIV-1 plasma samples of recently infected men who have sex with men (MSM) were amplified and sequenced. Multiple subtypes were identified by phylogenetic analyses of HIV-1 gag, env, and pol gene regions, including CRF01_AE (56.0%), CRF07_BC (30.0%), subtype B (12.0%), and unique recombinant forms (URFs, 6.0%). CRF01_AE was the most frequent genotype in the epidemic. Three recombination patterns of URFs were identified: 01BC, 01B, and 01C. The rate of HIV-1 transmitted drug resistance (TDR) mutation (M46L) was 2.08% (1/48). URFs and TDR first identified in this study suggest that HIV-1 prevalence is more and more complicated, and HIV-1 drug-resistant strains have begun to spread among at risk populations in Hebei. Our findings can provide vital information for an efficient surveillance system and strategic HIV prevention and control measures in China by revealing the evolutionary status and HIV-1 TDR of HIV-1 strains among recently infected MSM in Hebei Province.
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Affiliation(s)
- Xinli Lu
- College of Biology Science, Hebei University, Baoding, People's Republic of China
- Hebei Province Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
| | - Xianjiang Kang
- College of Biology Science, Hebei University, Baoding, People's Republic of China
| | - Suliang Chen
- Hebei Province Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
| | - Hongru Zhao
- Hebei Province Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Cuiying Zhao
- Hebei Province Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
| | - Yuqi Zhang
- Hebei Province Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Ze Cui
- Hebei Province Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
| | - Xianfeng Wang
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
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Tarosso LF, Sanabani SS, Ribeiro SP, Sauer MM, Tomiyama HI, Sucupira MC, Diaz RS, Sabino EC, Kalil J, Kallas EG. Short communication: HIV type 1 subtype BF leads to faster CD4+ T cell loss compared to subtype B. AIDS Res Hum Retroviruses 2014; 30:190-4. [PMID: 23906381 DOI: 10.1089/aid.2012.0243] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Although it has been suggested that biological differences among HIV-1 subtypes exist, their possible influence on disease progression has not been fully revealed. In particular, the increasing emergence of recombinants stresses the need to characterize disease presentation in persons infected by these diverse HIV-1 forms. We explored this issue among 83 Brazilian subjects infected with either HIV-1 subtype B or recombinant subtype BF, all followed since incident infection in a cohort study. Viral subtypes were assigned by full length sequencing of HIV-1 genomes. We observed that the baseline measures for CD4(+) T cells and viral load did not differ between the groups. However, longitudinal analysis revealed that subtype BF was clearly associated with a faster CD4(+) T cell decline compared to infection with subtype B, in spite of a similar plasma HIV-1 load. While subtype B-infected subjects presented a loss of 3.6 CD4(+) T cells/μl per month, subtype BF-infected individuals showed a monthly decay of 6.3 CD4(+) T cells/μl (p<0.01). The time to reach 350 CD4(+) T cells/μl and the time to start antiretroviral treatment were also shorter in subtype BF-infected persons. The elucidation of an accelerated CD4(+) T cell loss associated with subtype BF suggests that this HIV-1 genetic form could be more pathogenic than subtype B.
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Affiliation(s)
- Leandro F. Tarosso
- Division of Clinical Immunology and Allergy, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Sabri S. Sanabani
- Clinical Laboratory, Department of Pathology, LIM 03, Hospital das Clínicas (HC), School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Susan P. Ribeiro
- Division of Clinical Immunology and Allergy, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Mariana M. Sauer
- Division of Clinical Immunology and Allergy, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Helena I. Tomiyama
- Division of Clinical Immunology and Allergy, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Maria C. Sucupira
- Department of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - Ricardo S. Diaz
- Department of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - Ester C. Sabino
- Department of Infectious Diseases, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Jorge Kalil
- Division of Clinical Immunology and Allergy, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Esper G. Kallas
- Division of Clinical Immunology and Allergy, School of Medicine, University of São Paulo, São Paulo, Brazil
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Wirtz AL, Walker DG, Bollinger L, Sifakis F, Baral S, Johns B, Oelrichs R, Beyrer C. Modelling the impact of HIV prevention and treatment for men who have sex with men on HIV epidemic trajectories in low- and middle-income countries. Int J STD AIDS 2013; 24:18-30. [PMID: 23512511 DOI: 10.1177/0956462412472291] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Little is known about the impact of combination HIV prevention interventions for men who have sex with men (MSM) and the impacts on the wider epidemics. Modelling analyses of MSM-specific interventions across varied HIV epidemics may inform evidence-based responses. The Goals model was adapted to project the impacts of providing HIV interventions for MSM and access to expanded coverage of antiretroviral therapy (ART) for adults to measure the effects on the MSM and adult epidemics in Peru, Ukraine, Kenya and Thailand. Positive impacts were observed in all four countries. Across epidemics, 14-25% of infections among MSM may be averted between 2012 and 2016 when MSM interventions are brought to scale and MSM have equal access to expanded ART for adults. Among adults, MSM interventions may avert up to 4000 new infections, in addition to the benefits associated with increased ART. Greatest impacts from expanded interventions were observed in countries where same sex transmission contributes significantly to the HIV epidemic. While significant benefits are observed among the adult and MSM populations with expansion of ART, consideration should be given to the synergies of combining ART expansion with targeted interventions to reach hidden, high-risk populations for HIV testing and counselling and linkages to care.
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Affiliation(s)
- A L Wirtz
- Center for Public Health and Human Rights, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street E 71443, Baltimore, MD21205
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Freitas FB, Esteves A, Piedade J, Parreira R. Novel multiregion hybridization assay for the identification of the most prevalent genetic forms of the human immunodeficiency virus type 1 circulating in Portugal. AIDS Res Hum Retroviruses 2013; 29:318-28. [PMID: 22935093 DOI: 10.1089/aid.2012.0025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The most efficient method for HIV-1 genetic characterization involves full-genome sequencing, but the associated costs, technical features, and low throughput preclude it from being routinely used for the analysis of large numbers of viral strains. Multiregion hybridization assays (MHA) represent an alternative for a consistent genetic analysis of large numbers of viral strains. Classically, MHA rely on the amplification by real-time PCR of several regions scattered along the HIV-1 genome, and on their characterization with clade-specific TaqMan probes (also known as hydrolysis probes). In this context, the aim of our study was the development of a technical variant of an MHA (vMHA(B/G/02)) for genotyping the most prevalent genetic forms of HIV-1 circulating in Portugal. Different sets of primers were designed for universal and clade-specific amplifications of several sections of the viral genome: gag, pol(Pr), pol(RT), vpu, env(gp120), and env(gp41). vMHA(B/G/02) was implemented using a real-time PCR-based approach, with detection dependent on the use of SYBR Green I. As an alternative, a technically less demanding strategy based on conventional PCR and agarose gel analysis of the reaction products was also developed. This method performed with overall good sensitivity and specificity (>91%) when a convenience sample of 45 plasma-derived HIV-1 strains was analyzed. Apart from the detection of subtype B, G, CRF02_AG, and CRF14_BG viruses, several unique B/G recombinant were also detected. Curiously, recombinant viruses including CRF02_AG sequences were not detected in the group of samples analyzed.
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Affiliation(s)
- Ferdinando B. Freitas
- Unidade de Microbiologia Médica-Grupo de Virologia/Unidade de Parasitologia e Microbiologia Médicas, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Aida Esteves
- Unidade de Microbiologia Médica-Grupo de Virologia/Unidade de Parasitologia e Microbiologia Médicas, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - João Piedade
- Unidade de Microbiologia Médica-Grupo de Virologia/Unidade de Parasitologia e Microbiologia Médicas, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Ricardo Parreira
- Unidade de Microbiologia Médica-Grupo de Virologia/Unidade de Parasitologia e Microbiologia Médicas, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
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Quinn R, Salvatierra J, Solari V, Calderon M, Ton TG, Zunt JR. Human papillomavirus infection in men who have sex with men in Lima, Peru. AIDS Res Hum Retroviruses 2012; 28:1734-8. [PMID: 22519744 DOI: 10.1089/aid.2011.0307] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Human papillomavirus (HPV) infection among men who have sex with men (MSM) is the primary risk factor for anal cancer. Of 105 Peruvian MSM examined, 77.1% were infected with HPV; of these 79.0% were coinfected with two or more types and 47.3% were infected by a carcinogenic type. HPV types 53, 6, 16, and 58 were the most frequent HPV infections detected. High-risk HPV type infection was associated with sex work, HIV status, and having rectal chlamydial or gonorrheal infection. These findings support broadening HPV vaccine coverage and increasing surveillance for the development of cancer in MSM infected with HPV.
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Affiliation(s)
- Roswell Quinn
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah
| | | | | | | | - Thanh G.N. Ton
- Department of Neurology, University of Washington School of Medicine, Seattle, Washington
| | - Joseph R. Zunt
- Department of Neurology, University of Washington School of Medicine, Seattle, Washington
- Departments of Global Health, Medicine (Infectious Diseases), and Epidemiology, University of Washington School of Medicine, Seattle, Washington
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Yabar CA, Acuña M, Gazzo C, Salinas G, Cárdenas F, Valverde A, Romero S. New subtypes and genetic recombination in HIV type 1-infecting patients with highly active antiretroviral therapy in Peru (2008-2010). AIDS Res Hum Retroviruses 2012; 28:1712-22. [PMID: 22559065 DOI: 10.1089/aid.2012.0040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV-1 subtype B is the most frequent strain in Peru. However, there is no available data about the genetic diversity of HIV-infected patients receiving highly active antiretroviral therapy (HAART) here. A group of 267 patients in the Peruvian National Treatment Program with virologic failure were tested for genotypic evidence of HIV drug resistance at the Instituto Nacional de Salud (INS) of Peru between March 2008 and December 2010. Viral RNA was extracted from plasma and the segments of the protease (PR) and reverse transcriptase (RT) genes were amplified by reverse transcriptase polymerase chain reaction (RT-PCR), purified, and fully sequenced. Consensus sequences were submitted to the HIVdb Genotypic Resistance Interpretation Algorithm Database from Stanford University, and then aligned using Clustal X v.2.0 to generate a phylogenetic tree using the maximum likelihood method. Intrasubtype and intersubtype recombination analyses were performed using the SCUEAL program (Subtype Classification by Evolutionary ALgo-rithms). A total of 245 samples (91%) were successfully genotyped. The analysis obtained from the HIVdb program showed 81.5% resistance cases (n=198). The phylogenetic analysis revealed that subtype B was predominant in the population (98.8%), except for new cases of A, C, and H subtypes (n=4). Of these cases, only subtype C was imported. Likewise, recombination analysis revealed nine intersubtype and 20 intrasubtype recombinant cases. This is the first report of the presence of HIV-1 subtypes C and H in Peru. The introduction of new subtypes and circulating recombinants forms can make it difficult to distinguish resistance profiles in patients and consequently affect future treatment strategies against HIV in this country.
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Affiliation(s)
| | - Maribel Acuña
- Laboratorio de VETS/VIH-SIDA, Instituto Nacional de Salud, Lima, Peru
| | - Cecilia Gazzo
- Laboratorio de VETS/VIH-SIDA, Instituto Nacional de Salud, Lima, Peru
| | - Gabriela Salinas
- Laboratorio de VETS/VIH-SIDA, Instituto Nacional de Salud, Lima, Peru
| | - Fanny Cárdenas
- Laboratorio de VETS/VIH-SIDA, Instituto Nacional de Salud, Lima, Peru
| | - Ada Valverde
- Laboratorio de VETS/VIH-SIDA, Instituto Nacional de Salud, Lima, Peru
| | - Soledad Romero
- Laboratorio de VETS/VIH-SIDA, Instituto Nacional de Salud, Lima, Peru
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Rodríguez AM, Pascutti MF, Maeto C, Falivene J, Holgado MP, Turk G, Gherardi MM. IL-12 and GM-CSF in DNA/MVA immunizations against HIV-1 CRF12_BF Nef induced T-cell responses with an enhanced magnitude, breadth and quality. PLoS One 2012; 7:e37801. [PMID: 22655069 PMCID: PMC3360004 DOI: 10.1371/journal.pone.0037801] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 04/27/2012] [Indexed: 01/12/2023] Open
Abstract
In Argentina, the HIV epidemic is characterized by the co-circulation of subtype B and BF recombinant viral variants. Nef is an HIV protein highly variable among subtypes, making it a good tool to study the impact of HIV variability in the vaccine design setting. We have previously reported a specific cellular response against NefBF with low cross-reactivity to NefB in mice. The aim of this work was to analyze whether the co-administration of IL-12 and GM-CSF, using DNA and MVA vaccine vectors, could improve the final cellular response induced. Mice received three DNA priming doses of a plasmid that express NefBF plus DNAs expressing IL-12 and/or GM-CSF. Afterwards, all the groups were boosted with a MVAnefBF dose. The highest increase in the magnitude of the NefBF response, compared to that induced in the control was found in the IL-12 group. Importantly, a response with higher breadth was detected in groups which received IL-12 or GM-CSF, evidenced as an increased frequency of recognition of homologous (BF) and heterologous (B) Nef peptides, as well as a higher number of other Nef peptide pools representing different viral subtypes. However, these improvements were lost when both DNA cytokines were simultaneously administered, as the response was focused against the immunodominant peptide with a detrimental response towards subdominant epitopes. The pattern of cytokines secreted and the specific-T-cell proliferative capacity were improved in IL-12 and IL-12+GM-CSF groups. Importantly IL-12 generated a significant higher T-cell avidity against a B heterologous peptide. This study indicates that the incorporation of DNA expressing IL-12 in DNA/MVA schemes produced the best results in terms of improvements of T-cell-response key properties such as breadth, cross-reactivity and quality (avidity and pattern of cytokines secreted). These relevant results contribute to the design of strategies aimed to induce T-cell responses against HIV antigens with higher quality.
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Affiliation(s)
| | | | | | | | | | | | - María Magdalena Gherardi
- Centro Nacional de Referencia para el SIDA, Universidad de Buenos Aires, Buenos Aires, Argentina
- * E-mail:
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Guimarães ML, Velarde-Dunois KG, Segurondo D, Morgado MG. The HIV-1 epidemic in Bolivia is dominated by subtype B and CRF12_BF "family" strains. Virol J 2012; 9:19. [PMID: 22248191 PMCID: PMC3285048 DOI: 10.1186/1743-422x-9-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 01/16/2012] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Molecular epidemiological studies of HIV-1 in South America have revealed the occurrence of subtypes B, F1 and BF1 recombinants. Even so, little information concerning the HIV-1 molecular epidemiology in Bolivia is available. In this study we performed phylogenetic analyses from samples collected in Bolivia at two different points in time over a 10 year span. We analyzed these samples to estimate the trends in the HIV subtype and recombinant forms over time. MATERIALS AND METHODS Fifty one HIV-1 positive samples were collected in Bolivia over two distinct periods (1996 and 2005). These samples were genetically characterized based on partial pol protease/reverse transcriptase (pr/rt) and env regions. Alignment and neighbor-joining (NJ) phylogenetic analyses were established from partial env (n = 37) and all pol sequences using Mega 4. The remaining 14 env sequences from 1996 were previously characterized based on HMA-env (Heteroduplex mobility assay). The Simplot v.3.5.1 program was used to verify intragenic recombination, and SplitsTree 4.0 was employed to confirm the phylogenetic relationship of the BF1 recombinant samples. RESULTS Phylogenetic analysis of both env and pol regions confirmed the predominance of "pure" subtype B (72.5%) samples circulating in Bolivia and revealed a high prevalence of BF1 genotypes (27.5%). Eleven out of 14 BF1 recombinants displayed a mosaic structure identical or similar to that described for the CRF12_BF variant, one sample was classified as CRF17_BF, and two others were F1pol/Benv. No "pure" HIV-1 subtype F1 or B" variant of subtype B was detected in the present study. Of note, samples characterized as CRF12_BF-related were depicted only in 2005. CONCLUSION HIV-1 genetic diversity in Bolivia is mostly driven by subtype B followed by BF1 recombinant strains from the CRF12_BF "family". No significant temporal changes were detected between the mid-1990s and the mid-2000s for subtype B (76.2% vs 70.0%) or BF1 recombinant (23.8% vs 30.0%) samples from Bolivia.
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Affiliation(s)
- Monick L Guimarães
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil.
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15
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Junqueira DM, de Medeiros RM, Matte MCC, Araújo LAL, Chies JAB, Ashton-Prolla P, Almeida SEDM. Reviewing the history of HIV-1: spread of subtype B in the Americas. PLoS One 2011; 6:e27489. [PMID: 22132104 PMCID: PMC3223166 DOI: 10.1371/journal.pone.0027489] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 10/18/2011] [Indexed: 11/22/2022] Open
Abstract
The dispersal of HIV-1 subtype B (HIV-1B) is a reflection of the movement of human populations in response to social, political, and geographical issues. The initial dissemination of HIV-1B outside Africa seems to have included the passive involvement of human populations from the Caribbean in spreading the virus to the United States. However, the exact pathways taken during the establishment of the pandemic in the Americas remain unclear. Here, we propose a geographical scenario for the dissemination of HIV-1B in the Americas, based on phylogenetic and genetic statistical analyses of 313 available sequences of the pol gene from 27 countries. Maximum likelihood and Bayesian inference methods were used to explore the phylogenetic relationships between HIV-1B sequences, and molecular variance estimates were analyzed to infer the genetic structure of the viral population. We found that the initial dissemination and subsequent spread of subtype B in the Americas occurred via a single introduction event in the Caribbean around 1964 (1950–1967). Phylogenetic trees present evidence of several primary outbreaks in countries in South America, directly seeded by the Caribbean epidemic. Cuba is an exception insofar as its epidemic seems to have been introduced from South America. One clade comprising isolates from different countries emerged in the most-derived branches, reflecting the intense circulation of the virus throughout the American continents. Statistical analysis supports the genetic compartmentalization of the virus among the Americas, with a close relationship between the South American and Caribbean epidemics. These findings reflect the complex establishment of the HIV-1B pandemic and contribute to our understanding between the migration process of human populations and virus diffusion.
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Affiliation(s)
- Dennis Maletich Junqueira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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The Use of Bioinformatics for Studying HIV Evolutionary and Epidemiological History in South America. AIDS Res Treat 2011; 2011:154945. [PMID: 22162803 PMCID: PMC3226295 DOI: 10.1155/2011/154945] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 08/19/2011] [Indexed: 12/03/2022] Open
Abstract
The South American human immunodeficiency virus type 1 (HIV-1) epidemic is driven by several subtypes (B, C, and F1) and circulating and unique recombinant forms derived from those subtypes. Those variants are heterogeneously distributed around the continent in a country-specific manner. Despite some inconsistencies mainly derived from sampling biases and analytical constrains, most of studies carried out in the area agreed in pointing out specificities in the evolutionary dynamics of the circulating HIV-1 lineages. In this paper, we covered the theoretical basis, and the application of bioinformatics methods to reconstruct the HIV spatial-temporal dynamics, unveiling relevant information to understand the origin, geographical dissemination and the current molecular scenario of the HIV epidemic in the continent, particularly in the countries of Southern Cone.
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Praparattanapan J, Tragoolpua Y, Pathom-aree W, Kotarathitithum W, Chaiwarith R, Nuntachit N, Sirisanthana T, Supparatpinyo K. Current molecular epidemiology and recombination of HIV type 1 subtypes in northern Thailand. AIDS Res Hum Retroviruses 2011; 27:1201-6. [PMID: 21449850 DOI: 10.1089/aid.2010.0257] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
HIV subtype characterization is an important tool to monitor the genetic variation of the HIV epidemic. This study investigated the current HIV subtype distribution and recombination among the northern Thai population. An in-house genotypic assay of HIV protease and reverse transcriptase genes was performed on 420 plasma specimens from HIV-infected patients residing in several northern Thai provinces. HIV subtyping was determined by phylogenetic analysis. Three hundred and ninety-eight sequences (94.8%) were identified as CRF01_AE with the genetic distance of 1.848 ± 0.957% and 12 (2.9%) as subtype B with the genetic distance of 4.186 ± 0.849%. In addition, two sequences (0.5%) of HIV subtype C were found, suggesting that these patients were either immigrants from another country or were infected through heterosexual contact with HIV-infected subjects from another country. Bootscan analysis showed that there were eight (1.9%) unique recombinant forms (URFs) consisting of a recombinant of CRF01_AE with subtype B or subtype C. The information from this study is useful for prevention programs to halt the onward transmission of a particular HIV outbreak. However, characterization of the full genome of these CRF01_AE/B and CRF01_AE/C intersubtype recombinants, and also subtype C, is required for confirmation and elucidation.
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Affiliation(s)
- Jutarat Praparattanapan
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Yingmanee Tragoolpua
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Wasu Pathom-aree
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Wilai Kotarathitithum
- Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Romanee Chaiwarith
- Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Nontakan Nuntachit
- Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Thira Sirisanthana
- Research Institute for Health Science, Chiang Mai University, Chiang Mai, Thailand
| | - Khuanchai Supparatpinyo
- Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Research Institute for Health Science, Chiang Mai University, Chiang Mai, Thailand
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18
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Teixeira D, Munerato P, Komninakis SCV, Fusuma EE, Janini LM, Sucupira MCA, Diaz RS. The detection of in vivo and in vitro HIV type 1 B/F profiles in Brazil using a real-time PCR assay for five HIV type 1 genomic regions. AIDS Res Hum Retroviruses 2010; 26:981-90. [PMID: 20707640 DOI: 10.1089/aid.2010.0023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We sought to determine the frequency and profile of HIV-1 BF recombinants in vitro and in vivo. Laboratory HIV-1 strains from subtypes B and F were cocultured and evaluated. Clinical samples from the city of Santos, Brazil, where the first HIV-1 B/F circulating recombinant forms (CRF) were described, were also assessed. Five real-time PCR assays were developed to equally amplify subtypes B and F, and subtype-specific probes were developed and optimized. To validate the PCR systems, clinical samples from Santos were sequenced and phylogenetically analyzed. The real-time PCR assays were performed on these samples and on the supernatant of an in vitro competition assay to assess emergent recombinant strains. Out of 157 clinical samples, 62.1% were defined as subtype B, 3.0% were subtype F, 16.7% presented the CRF28_BF profile, and 13.6% of the samples presented the CRF29_BF profile. The specificity and sensitivity in the discrimination assay for this sample panel were 93% and 92%, respectively. The HIV that emerged from the coinfected cell culture closely resembled the CRF28_BF profile. The first-described CRFs are still fixed in this geographic region of Brazil, and the in vitro emerging strains detected by real-time PCR suggest that in addition to the shaping of recombinant strains by immune selection, viral structures may also play an important role in emerging CRFs.
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Affiliation(s)
- Daniela Teixeira
- Retrovirology Laboratory, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - Patricia Munerato
- Retrovirology Laboratory, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | | | - Erika Etsuko Fusuma
- Retrovirology Laboratory, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - Luiz Mario Janini
- Retrovirology Laboratory, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | | | - Ricardo Sobhie Diaz
- Retrovirology Laboratory, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
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Delgado E, Ríos M, Fernández J, Pérez-Álvarez L, Nájera R, Thomson MM. Identification of a new HIV type 1 BF intersubtype circulating recombinant form (CRF44_BF) in Chile. AIDS Res Hum Retroviruses 2010; 26:821-6. [PMID: 20618101 DOI: 10.1089/aid.2010.0006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
HIV-1 BF intersubtype recombinants are frequent in Argentina, Uruguay, and Brazil, where among a high diversity of BF unique recombinant forms (URFs), eight circulating recombinant forms (CRFs) have been characterized. Here, we describe a new one, designated CRF44_BF, identified in HIV-1 samples from Chile. In a previous report, where partial pol sequences of 136 HIV-1 infections of Chilean subjects were analyzed, a phylogenetic cluster of HIV-1 recombinant BF viruses from 10 individuals, with coincident intersubtype recombination points, was detected. One virus of this cluster had been characterized along its near full-length genome. A second one, from an epidemiologically unlinked HIV-1-infected subject, is described here. Both genomes share identical mosaic structures, consisting of a predominantly subtype F1 genome with three fragments of subtype B. Coincident breakpoints and phylogenetic clustering of the newly identified CRF44_BF with CRF12_BF, CRF17_BF, and CRF38_BF support a common origin of different CRF_BFs identified in Argentina, Uruguay, and Chile.
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Affiliation(s)
- Elena Delgado
- Unit of Biology and Variability of HIV, Spanish National Center of Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Maritza Ríos
- National Reference Center of HIV/AIDS, Public Health Institute of Chile, Santiago, Chile
| | - Jorge Fernández
- Laboratory of Molecular Genetics, Public Health Institute of Chile, Santiago, Chile
| | - Lucía Pérez-Álvarez
- Unit of Biology and Variability of HIV, Spanish National Center of Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Rafael Nájera
- Unit of Biology and Variability of HIV, Spanish National Center of Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Michael M. Thomson
- Unit of Biology and Variability of HIV, Spanish National Center of Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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Beyrer C, Baral SD, Walker D, Wirtz AL, Johns B, Sifakis F. The Expanding Epidemics of HIV Type 1 Among Men Who Have Sex With Men in Low- and Middle-Income Countries: Diversity and Consistency. Epidemiol Rev 2010; 32:137-51. [DOI: 10.1093/epirev/mxq011] [Citation(s) in RCA: 160] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Bello G, Aulicino PC, Ruchansky D, Guimarães ML, Lopez-Galindez C, Casado C, Chiparelli H, Rocco C, Mangano A, Sen L, Morgado MG. Phylodynamics of HIV-1 circulating recombinant forms 12_BF and 38_BF in Argentina and Uruguay. Retrovirology 2010; 7:22. [PMID: 20307282 PMCID: PMC2854103 DOI: 10.1186/1742-4690-7-22] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Accepted: 03/22/2010] [Indexed: 11/10/2022] Open
Abstract
Background Although HIV-1 CRF12_BF and CRF38_BF are two epidemiologically important recombinant lineages circulating in Argentina and Uruguay, little is known about their population dynamics. Methods A total of 120 "CRF12_BF-like" and 20 "CRF38_BF-like" pol recombinant sequences collected in Argentina and Uruguay from 1997 to 2009 were subjected to phylogenetic and Bayesian coalescent-based analyses to estimate evolutionary and demographic parameters. Results Phylogenetic analyses revealed that CRF12_BF viruses from Argentina and Uruguay constitute a single epidemic with multiple genetic exchanges among countries; whereas circulation of the CRF38_BF seems to be confined to Uruguay. The mean estimated substitution rate of CRF12_BF at pol gene (2.5 × 10-3 substitutions/site/year) was similar to that previously described for subtype B. According to our estimates, CRF12_BF and CRF38_BF originated at 1983 (1978-1988) and 1986 (1981-1990), respectively. After their emergence, the CRF12_BF and CRF38_BF epidemics seem to have experienced a period of rapid expansion with initial growth rates of around 1.2 year-1 and 0.9 year-1, respectively. Later, the rate of spread of these CRFs_BF seems to have slowed down since the mid-1990s. Conclusions Our results suggest that CRF12_BF and CRF38_BF viruses were generated during the 1980s, shortly after the estimated introduction of subtype F1 in South America (~1975-1980). After an initial phase of fast exponential expansion, the rate of spread of both CRFs_BF epidemics seems to have slowed down, thereby following a demographic pattern that resembles those previously reported for the HIV-1 epidemics in Brazil, USA, and Western Europe.
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Affiliation(s)
- Gonzalo Bello
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil.
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Tovanabutra S, Sanders EJ, Graham SM, Mwangome M, Peshu N, McClelland RS, Muhaari A, Crossler J, Price MA, Gilmour J, Michael NL, McCutchan FM. Evaluation of HIV type 1 strains in men having sex with men and in female sex workers in Mombasa, Kenya. AIDS Res Hum Retroviruses 2010; 26:123-31. [PMID: 20156095 DOI: 10.1089/aid.2009.0115] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We compared HIV-1 strains in incident and prevalent infections in a cohort of men having sex with men (MSM) and female sex workers (FSW) near Mombasa, Kenya and conducted a cross-sectional study of viral isolates from a sample of HIV-1-infected MSM and FSW in Kilifi, Coast Province, Kenya. RNA extracted from plasma of 13 MSM, 9 FSW, and one heterosexual male was amplified by nested RT-PCR and the products were directly sequenced. HIV-1 strains from 21 individuals were characterized with one or more complete genome sequences, and two were sequenced in the Nef gene. The envelope quasispecies was also studied in one individual. Among MSM, eight strains were subtype A and five were recombinant. There were two epidemiologically linked pairs of sequences; one pair was subtype A and the other pair was a complex AA2CD recombinant of identical structure. Another MSM was dually infected with DG recombinant strains of related, but nonidentical, structure. MSM also harbored AC and AD recombinant strains. The FSW harbored seven subtype A strains, an AD recombinant, and an AA2D strain related to CRF16_A2D. The one heterosexual male studied had a subtype A infection. This MSM epidemic in Kenya appears to be of local origin, harboring many strains typical of the broader Kenyan epidemic. Characteristics of a close social network were identified, with extended chains of transmission, novel recombinant strains possibly generated within the network, and a relatively high proportion of recombinant and dual infections.
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Affiliation(s)
- Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland 20850
| | - Eduard J. Sanders
- Centre for Geographic Medicine Research–Coast, Kenya Medical Research Institute (KEMRI), Kilifi, Kenya
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Headington, UK
| | - Susan M. Graham
- Centre for Geographic Medicine Research–Coast, Kenya Medical Research Institute (KEMRI), Kilifi, Kenya
- University of Washington, Seattle, Washington 98109
| | - Mary Mwangome
- Centre for Geographic Medicine Research–Coast, Kenya Medical Research Institute (KEMRI), Kilifi, Kenya
| | - Norbert Peshu
- Centre for Geographic Medicine Research–Coast, Kenya Medical Research Institute (KEMRI), Kilifi, Kenya
| | | | - Allan Muhaari
- Centre for Geographic Medicine Research–Coast, Kenya Medical Research Institute (KEMRI), Kilifi, Kenya
| | - Jacqueline Crossler
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland 20850
| | - Matt A. Price
- International AIDS Vaccine Initiative, New York, New York 10038
| | - Jill Gilmour
- International AIDS Vaccine Initiative, New York, New York 10038
| | - Nelson L. Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland 20850
| | - Francine M. McCutchan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland 20850
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Abstract
PURPOSE OF REVIEW This review attempts to acquaint the reader with the molecular epidemiology of HIV-1 and to describe some of the more promising approaches to vaccine development in the light of this diversity. RECENT FINDINGS The primary genetic forms of HIV-1 in the world today are subtypes A, B, C, CRF01-AE and CRF02-AG. In sub-Saharan Africa, subtypes A and C and CRF02-AG account for most of the infections. In Asia, there are subtypes B, C and CRF01 AE. Europe, the Americas and the Caribbean are dominated by subtype B, and subtype A is in the former Soviet Union. While the genetic diversity of HIV-1 in the world can seem daunting, the vast majority of infections are actually caused by one of these five genetic forms. Approaches to dealing with this in the development of vaccines include targeting conserved regions of the genome, creating ancestral forms of the virus or putting many different forms together into a cocktail. Each of these approaches shows promise. To optimize the chances of initially showing efficacy in HIV vaccine trials, the genetic form of the vaccine strains will resemble those of the circulating strains in the target population. Once efficacy is demonstrated, however, it will be possible to determine whether genetic subtype is at all predictive of vaccine protection. SUMMARY Although the genetic diversity of HIV-1 is impressive, it is not limitless. Most of the infections worldwide are actually due to a handful of strains. It should be possible for a few vaccine strategies to conquer HIV-1 definitively.
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Gronewold TMA, Baumgartner A, Hierer J, Sierra S, Blind M, Schäfer F, Blümer J, Tillmann T, Kiwitz A, Kaiser R, Zabe-Kühn M, Quandt E, Famulok M. Kinetic binding analysis of aptamers targeting HIV-1 proteins by a combination of a microbalance array and mass spectrometry (MAMS). J Proteome Res 2009; 8:3568-77. [PMID: 19469583 DOI: 10.1021/pr900265r] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
An enhanced chip-based detection platform was developed by integrating a surface acoustic wave biosensor of the Love-wave type with protein identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS). The system was applied to characterize the interaction of aptamers with their cognate HIV-1 proteins. The aptamers, which target two proteins of HIV-1, were identified using an automated in vitro selection platform. For aptamers S66A-C6 and S68B-C5, which target the V3 loop of the HIV-1 envelope protein gp120, KD values of 406 and 791 nM, respectively, were measured. Aptamer S69A-C15 was shown to bind HIV-1 reverse transcriptase (HIV-1 RT) with a KD value of 637 nM when immobilized on the biosensor surface. HIV-1 RT was identified with high significance using MALDI-ToF MS even in crude protein mixtures. The V3-loop of gp120 could be directly identified when using chip-bound purified protein samples. From crude protein mixtures, it could be identified indirectly with high significance via its fusion-partner glutathione-S-transferase (GST). Our data show that the combination of the selectivity of aptamers with a sensitive detection by MS enables the reliable and quantitative analysis of kinetic binding events of protein solutions in real time.
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Characterization of DNA and MVA vectors expressing Nef from HIV-1 CRF12_BF revealed high immune specificity with low cross-reactivity against subtype B. Virus Res 2009; 146:1-12. [PMID: 19715734 DOI: 10.1016/j.virusres.2009.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Revised: 08/06/2009] [Accepted: 08/20/2009] [Indexed: 11/20/2022]
Abstract
The HIV epidemic in Argentina is characterized by the high prevalence of infections caused by subtype B and BF variants. In this study, the Nef protein was used as a tool to study the impact of HIV-1 BF variants in the design of future vaccines. DNA and MVA vectors expressing Nef of the CRF12_BF recombinant form of HIV-1 were generated and characterized. After the administration of single DNAprime/MVAboost immunization schedules in Balb/c mice we found that NefBF delivered from these vectors generated a response of high specificity with low cross-reactivity against subtype B. But, when a more potent response was induced after 3 priming DNA doses and a booster with MVA virus, cross-reactivity against NefB was detected, although of lower magnitude than the NefBF specific. These results will be pivotal for vaccines designs in our region, indicating that antigens from these viral variants must be considered for a future vaccine.
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Carrión AG, Laguna-Torres VA, Soto-Castellares G, Castillo M, Salazar E, Negron E, Kolevic L, Montano SM, Sánchez JL, Bautista CT, Oberhelman RA, Kochel TJ. Molecular characterization of the human immunodeficiency virus type 1 among children in Lima, Peru. AIDS Res Hum Retroviruses 2009; 25:833-5. [PMID: 19678768 DOI: 10.1089/aid.2009.0016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In Peru, there is a lack of information on molecular analysis in pediatric human immunodeficiency virus (HIV) infection. At present, the mother-to-child transmission rate is estimated at approximately 2-4%. The objective of this study was to assess the molecular epidemiology of HIV-1 in infected children. Children with suspected or confirmed pulmonary tuberculosis were evaluated at two public hospitals between 2002 and 2007. Whole blood samples were obtained from 90 HIV-positive children, who were confirmed to be positive by enzyme-linked immunosorbent assay and Western blot. The specimens were subjected to envelope heteroduplex mobility assay (env HMA) followed by gag and pol gene region sequence analysis. Subtype B was found in 88 (98%) of 90 children and 2 (2%) children were subtype BF recombinants. This is the first report of recombinant HIV strains in HIV-infected children in Peru. Understanding the origin, diversity, and spread of HIV strains worldwide will be necessary for the development of an effective vaccine that targets pediatric populations throughout the world.
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Affiliation(s)
- A G Carrión
- U.S. Naval Medical Research Center Detachment (NMRCD), Lima, Perú
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27
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The National Response to the HIV/AIDS Epidemic in Peru: Accomplishments and Gaps-A Review. J Acquir Immune Defic Syndr 2009; 51 Suppl 1:S60-6. [DOI: 10.1097/qai.0b013e3181a66208] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Close phylogenetic relationship between Angolan and Romanian HIV-1 subtype F1 isolates. Retrovirology 2009; 6:39. [PMID: 19386115 PMCID: PMC2680801 DOI: 10.1186/1742-4690-6-39] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Accepted: 04/22/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Here, we investigated the phylogenetic relationships of the HIV-1 subtype F1 circulating in Angola with subtype F1 strains sampled worldwide and reconstructed the evolutionary history of this subtype in Central Africa. METHODS Forty-six HIV-1-positive samples were collected in Angola in 2006 and subtyped at the env-gp41 region. Partial env-gp120 and pol-RT sequences and near full-length genomes from those env-gp41 subtype F1 samples were further generated. Phylogenetic analyses of partial and full-length subtype F1 strains isolated worldwide were carried out. The onset date of the subtype F1 epidemic in Central Africa was estimated using a Bayesian Markov chain Monte Carlo approach. RESULTS Nine Angolan samples were classified as subtype F1 based on the analysis of the env-gp41 region. All nine Angolan sequences were also classified as subtype F1 in both env-gp120 and pol-RT genomic regions, and near full-length genome analysis of four of these samples confirmed their classification as "pure" subtype F1. Phylogenetic analyses of subtype F1 strains isolated worldwide revealed that isolates from the Democratic Republic of Congo (DRC) were the earliest branching lineages within the subtype F1 phylogeny. Most strains from Angola segregated in a monophyletic group together with Romanian sequences; whereas South American F1 sequences emerged as an independent cluster. The origin of the subtype F1 epidemic in Central African was estimated at 1958 (1934-1971). CONCLUSION "Pure" subtype F1 strains are common in Angola and seem to be the result of a single founder event. Subtype F1 sequences from Angola are closely related to those described in Romania, and only distantly related to the subtype F1 lineage circulating in South America. Original diversification of subtype F1 probably occurred within the DRC around the late 1950s.
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Ruchansky D, Casado C, Russi JC, Arbiza JR, Lopez-Galindez C. Identification of a new HIV Type 1 circulating recombinant form (CRF38_BF1) in Uruguay. AIDS Res Hum Retroviruses 2009; 25:351-6. [PMID: 19327055 DOI: 10.1089/aid.2008.0248] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recombination has been shown to be an important force in HIV-1 evolution. Recombination contributes to an increase in genetic variation and hinders vaccine design efforts. Several molecular epidemiology studies in South America described the circulation of subtypes B, F, and C as well as several B/F1 recombinants. This study performed by nucleotide sequencing in at least two genes of 89 samples from Uruguay has shown a complex HIV-1 epidemic characterized by the cocirculation of subtype B, and subtype C strains, together with an important group of BF1 recombinant viruses, including isolates similar to CRF12_BF. In addition we identified a new circulating recombinant form, designated CRF38_BF(1), which was dominant in the recombinant virus group.
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Affiliation(s)
- Dora Ruchansky
- Servicio de Virología Molecular, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- Laboratorio Nacional de Referencia VIH-SIDA, Servicio Nacional de Laboratorios de Salud Publica del Ministerio de Salud Publica, Montevideo, Uruguay
- Sección Virología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Concepción Casado
- Servicio de Virología Molecular, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - José C. Russi
- Laboratorio Nacional de Referencia VIH-SIDA, Servicio Nacional de Laboratorios de Salud Publica del Ministerio de Salud Publica, Montevideo, Uruguay
| | - Juan R. Arbiza
- Sección Virología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Cecilio Lopez-Galindez
- Servicio de Virología Molecular, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
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30
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Ahumada-Ruiz S, Casado C, Toala-González I, Flores-Figueroa D, Rodríguez-French A, López-Galíndez C. High divergence within the major HIV type 1 subtype B epidemic in Panama. AIDS Res Hum Retroviruses 2008; 24:1461-6. [PMID: 19000026 DOI: 10.1089/aid.2008.0153] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The first molecular epidemiology study of human immunodeficiency virus type 1 (HIV-1) in Panama has been performed with plasma samples from 66 AIDS patients infected by different transmission routes and obtained from distinct locations. All samples were amplified by RT-PCR and sequenced in gag (p17) and env (C2-C4) genes. Phylogenetic analyses revealed that 64 (97%) of the samples belong to subtype B. We also identified the presence of two CRF, one CRF12_BF and one CRF02_AG. The most notable feature of the subtype B epidemic in Panama was the large genetic distance among isolates with a mean of 15.2% but reaching up to 31.3 % in env, indicating an epidemic with a long period of evolution.
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Affiliation(s)
- Sara Ahumada-Ruiz
- Servicio de Virología Molecular, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- Laboratorio de Microbiología Experimental y Aplicada, Vicerrectoria de Investigación y Posgrado, Universidad de Panamá, Panama City, Panama
| | - Concepción Casado
- Servicio de Virología Molecular, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Iván Toala-González
- Sala de Infectología, Complejo Hospitalario Dr. Arnulfo Arias Madrid, Caja del Seguro Social de Panamá, Panama City, Panama
| | - Dario Flores-Figueroa
- Sala de Infectología, Complejo Hospitalario Dr. Arnulfo Arias Madrid, Caja del Seguro Social de Panamá, Panama City, Panama
| | | | - Cecilio López-Galíndez
- Servicio de Virología Molecular, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
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31
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Yabar CA, Salvatierra J, Quijano E. Polymorphism, recombination, and mutations in HIV type 1 gag-infecting Peruvian male sex workers. AIDS Res Hum Retroviruses 2008; 24:1405-13. [PMID: 19000025 DOI: 10.1089/aid.2008.0130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV genetic diversity in female sex workers (FSW) has been previously described in Peru; however this information is not yet available for male sex workers (MSW). Therefore, purified peripheral blood mononuclear cell DNA from 147 HIV-infected subjects identified as MSW and FSW was used to amplify a 460-bp fragment corresponding to the p24-p7 region of the gag gene. The PCR product was digested with restriction enzymes to identify genetic polymorphism. Later, a random group of samples (n = 19) was sequenced to perform phylogenetic analysis, intragenic recombination analysis, and deleterious mutations leading to a nonfunctional protein in conservative regions of the Gag protein. RFLP analysis revealed 11 genetic variants for AluI and five for MspI. A group of nonsex workers (NSW) used for comparison showed different RFLP genetic variant distributions. Of interest, nine cases of mixed genetic variants were observed for MSW, one case for FSW, and none for NSW. Phylogenetic analysis revealed that all HIV-1 species were subtype B. Intragenic recombination analysis showed a B/C recombination case from an FSW (boostrap = 1000; p value < 0.05). Of interest, deleterious mutations were observed in three cases of conservative D2 zinc domains for Gag 3/19 and one case of the high homology region (1/19). This study shows that gag of HIV circulating from MSW has high genetic polymorphism involving deleterious mutations in conserved domains from the p24-p7 gag region.
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Affiliation(s)
- Carlos Augusto Yabar
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Peru
| | - Javier Salvatierra
- Centro Especializado en Enfermedades de Transmisión Sexual “Alberto Barton,” Callao, Peru
| | - Eberth Quijano
- Centro Especializado en Enfermedades de Transmisión Sexual “Alberto Barton,” Callao, Peru
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Dumans AT, Barreto CC, Santos AF, Arruda M, Sousa TM, Machado ES, Sabino EC, Brindeiro RM, Tanuri A, Duarte AJ, Soares MA. Distinct resistance mutation and polymorphism acquisition in HIV-1 protease of subtypes B and F1 from children and adult patients under virological failure. INFECTION GENETICS AND EVOLUTION 2008; 9:62-70. [PMID: 18992847 DOI: 10.1016/j.meegid.2008.10.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2008] [Revised: 10/06/2008] [Accepted: 10/08/2008] [Indexed: 01/30/2023]
Abstract
The goal of this work was to compare the differences between human immunodeficiency virus type 1 (HIV-1) of B and F1 subtypes in the acquisition of major and minor protease inhibitor (PI)-associated resistance mutations and of other polymorphisms at the protease (PR) gene, through a cross sectional study. PR sequences from subtypes B and F1 isolates matched according to PI exposure time from Brazilian patients were included in this study. Sequences were separated in four groups: 24 and 90 from children and 141 and 99 from adults infected with isolates of subtypes F1 and B, respectively. For comparison, 211 subtype B and 79 subtype F1 PR sequences from drug-naïve individuals were included. Demographic and clinical data were similar among B- and F1-infected patients. In untreated patients, mutations L10V, K20R, and M36I were more frequent in subtype F1, while L63P, A71T, and V77I were more prevalent in subtype B. In treated patients, K20M, D30N, G73S, I84V, and L90M, were more prevalent in subtype B, and K20T and N88S were more prevalent in subtype F1. A higher proportion of subtype F1 than of subtype B strains containing other polymorphisms was observed. V82L mutation was present with increased frequency in isolates from children compared to isolates from adults infected with both subtypes. We could observe a faster resistance emergence in children than in adults, during treatment with protease inhibitors. This data provided evidence that, although rates of overall drug resistance do not differ between subtypes B and F1, the former accumulates resistance at higher proportion in specific amino acid positions of protease when compared to the latter.
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Affiliation(s)
- Ana T Dumans
- Unidade de Genética e Biologia Molecular, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
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Drug resistance mutation profile and accumulation kinetics in human immunodeficiency virus-positive individuals infected with subtypes B and F failing highly active antiretroviral therapy are influenced by different viral codon usage patterns. Antimicrob Agents Chemother 2008; 52:4497-502. [PMID: 18838582 DOI: 10.1128/aac.00820-08] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The major human immunodeficiency virus type 1 subtype circulating in Brazil is B, followed by F and C. We have genotyped 882 samples from Brazilian patients for whom highly active antiretroviral therapy failed, and we found subtype B and the unique recombinant B/F1 forms circulating. Due to codon usage variation, there is a significantly lower incidence of the substitutions L210W, Q151M, and F116Y in subtype F1 isolates than in the subtype B counterparts.
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Magnitude, breadth, and functional profile of T-cell responses during human immunodeficiency virus primary infection with B and BF viral variants. J Virol 2008; 82:2853-66. [PMID: 18184702 DOI: 10.1128/jvi.02260-07] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The molecular pattern of the human immunodeficiency virus (HIV) epidemic in Argentina provides an appropriate scenario to study cellular immune responses in patients with non-clade B infection. We aimed to map T-cell responses in patients infected with BF recombinant variants and compare them with those of clade B patients. Sixteen recently infected patients were enrolled and grouped by viral subtype. Nef-specific responses were evaluated with a peptide matrix-based gamma interferon (IFN-gamma) enzyme-linked immunospot (ELISPOT) assay using B and BF overlapping peptides. Cross-clade and clade-specific responses were found. A correlation between B versus BF Nef-specific responses was identified. Detailed analysis at the single-peptide level revealed that BF patients show a narrower response but greater magnitude. Nef immunodominant responses agreed with previous publications, although the B loop was targeted at an unexpectedly high frequency. The putative HLA allele(s) restricting each positive response was determined. Single-peptide level screening with two different peptide sets uncovered discordant responses (mostly caused by peptide offsetting) and allowed detection of increased breadth. Positive responses identified by ELISPOT assay were further studied by intracellular cytokine staining. These were almost exclusively mediated by CD8 T cells. Characterization of concordant responses revealed that cells show distinct functional profiles, depending on the peptide presented. Last, quality (in terms of polyfunctionality) of T cells was associated with better viral replication containment. Overall, interclade differences in the frequency of epitopes recognized, structural domains targeted, and magnitude of responses were identified. Screening T-cell responses with multiple sets increased sensitivity. Further support for the notion of polyfunctional CD8(+) T-cell requirement to better control viral replication is also provided.
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35
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Sterjovski J, Churchill MJ, Ellett A, Gray LR, Roche MJ, Dunfee RL, Purcell DFJ, Saksena N, Wang B, Sonza S, Wesselingh SL, Karlsson I, Fenyo EM, Gabuzda D, Cunningham AL, Gorry PR. Asn 362 in gp120 contributes to enhanced fusogenicity by CCR5-restricted HIV-1 envelope glycoprotein variants from patients with AIDS. Retrovirology 2007; 4:89. [PMID: 18076768 PMCID: PMC2225424 DOI: 10.1186/1742-4690-4-89] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Accepted: 12/12/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND CCR5-restricted (R5) human immunodeficiency virus type 1 (HIV-1) variants cause CD4+ T-cell loss in the majority of individuals who progress to AIDS, but mechanisms underlying the pathogenicity of R5 strains are poorly understood. To better understand envelope glycoprotein (Env) determinants contributing to pathogenicity of R5 viruses, we characterized 37 full-length R5 Envs from cross-sectional and longitudinal R5 viruses isolated from blood of patients with asymptomatic infection or AIDS, referred to as pre-AIDS (PA) and AIDS (A) R5 Envs, respectively. RESULTS Compared to PA-R5 Envs, A-R5 Envs had enhanced fusogenicity in quantitative cell-cell fusion assays, and reduced sensitivity to inhibition by the fusion inhibitor T-20. Sequence analysis identified the presence of Asn 362 (N362), a potential N-linked glycosylation site immediately N-terminal to CD4-binding site (CD4bs) residues in the C3 region of gp120, more frequently in A-R5 Envs than PA-R5 Envs. N362 was associated with enhanced fusogenicity, faster entry kinetics, and increased sensitivity of Env-pseudotyped reporter viruses to neutralization by the CD4bs-directed Env mAb IgG1b12. Mutagenesis studies showed N362 contributes to enhanced fusogenicity of most A-R5 Envs. Molecular models indicate N362 is located adjacent to the CD4 binding loop of gp120, and suggest N362 may enhance fusogenicity by promoting greater exposure of the CD4bs and/or stabilizing the CD4-bound Env structure. CONCLUSION Enhanced fusogenicity is a phenotype of the A-R5 Envs studied, which was associated with the presence of N362, enhanced HIV-1 entry kinetics and increased CD4bs exposure in gp120. N362 contributes to fusogenicity of R5 Envs in a strain dependent manner. Our studies suggest enhanced fusogenicity of A-R5 Envs may contribute to CD4+ T-cell loss in subjects who progress to AIDS whilst harbouring R5 HIV-1 variants. N362 may contribute to this effect in some individuals.
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Affiliation(s)
- Jasminka Sterjovski
- Macfarlane Burnet Institute for Medical Research & Public Health, Melbourne, Victoria, Australia.
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Véras NMC, Véras VS, Ramalho ED, Kyaw C, Silva RR, Brígido MM, Martins CR. HIV type 1 genetic variability in central Brazil. AIDS Res Hum Retroviruses 2007; 23:1481-90. [PMID: 18160005 DOI: 10.1089/aid.2007.0145] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This study analyzed the genes pol and env to determine the genetic variability of HIV-1 in Central Brazil. Forty-one isolates of HIV-1-infected individuals had protease, reverse transcriptase, and C2C3/ env amplified by nested PCR and sequenced. The subtype was determined by the program REGA and phylogenetic analyses. The samples identified as putative recombinant forms were analyzed by SimPlot. A high prevalence of subtype B (95.1%) was observed, followed by mosaic viruses B/F (4.9%). The amino acid sequences from 30 HIV-1 isolates were analyzed for the antigenic intrasubtype diversity. The most prevalent gp120 V3 loop motif was the GPGR (United States/Europe) (43.3%), described in B and F subtypes, followed by the GPGK tetrapeptide (10%). The Brazilian variant B" (GWGR), GFGR, and GLGR tetrapeptides were found in 6.7%. Other V3 variants were found in eight isolates (26.7%). Phylogenetic tree analysis was also performed in order to verify the relationship of the HIV-1 samples from Central Brazil with other HIV-1 sequences that circulate in Brazil. The subtype B sequences from Central Brazil formed a polyphyletic cluster in the tree, indicating that these strains are similar to those from other geographic regions. These results contribute to the understanding of HIV in Brazil, and may prove useful for the development of vaccine candidates.
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Affiliation(s)
- Nazle M. C. Véras
- Pós-Graduação em Biologia Molecular, Instituto de Biologia, Universidade de Brasília ICC Sul, 70919-900 Brasília, DF, Brazil
| | - Verônica S. Véras
- Pós-Graduação em Biologia Molecular, Instituto de Biologia, Universidade de Brasília ICC Sul, 70919-900 Brasília, DF, Brazil
| | - Eduardo D. Ramalho
- Pós-Graduação em Biologia Molecular, Instituto de Biologia, Universidade de Brasília ICC Sul, 70919-900 Brasília, DF, Brazil
| | - Cynthia Kyaw
- Pós-Graduação em Biologia Molecular, Instituto de Biologia, Universidade de Brasília ICC Sul, 70919-900 Brasília, DF, Brazil
| | - Ruiter R. Silva
- Laboratório Central de Saúde Pública do Distrito Federal, Brasília, DF, Brazil
| | - Marcelo M. Brígido
- Pós-Graduação em Biologia Molecular, Instituto de Biologia, Universidade de Brasília ICC Sul, 70919-900 Brasília, DF, Brazil
| | - Cláudia R.F. Martins
- Pós-Graduação em Biologia Molecular, Instituto de Biologia, Universidade de Brasília ICC Sul, 70919-900 Brasília, DF, Brazil
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Baral S, Sifakis F, Cleghorn F, Beyrer C. Elevated risk for HIV infection among men who have sex with men in low- and middle-income countries 2000-2006: a systematic review. PLoS Med 2007; 4:e339. [PMID: 18052602 PMCID: PMC2100144 DOI: 10.1371/journal.pmed.0040339] [Citation(s) in RCA: 500] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2007] [Accepted: 10/15/2007] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Recent reports of high HIV infection rates among men who have sex with men (MSM) from Asia, Africa, Latin America, and the former Soviet Union (FSU) suggest high levels of HIV transmission among MSM in low- and middle-income countries. To investigate the global epidemic of HIV among MSM and the relationship of MSM outbreaks to general populations, we conducted a comprehensive review of HIV studies among MSM in low- and middle-income countries and performed a meta-analysis of reported MSM and reproductive-age adult HIV prevalence data. METHODS AND FINDINGS A comprehensive review of the literature was conducted using systematic methodology. Data regarding HIV prevalence and total sample size was sequestered from each of the studies that met inclusion criteria and aggregate values for each country were calculated. Pooled odds ratio (OR) estimates were stratified by factors including HIV prevalence of the country, Joint United Nations Programme on HIV/AIDS (UNAIDS)-classified level of HIV epidemic, geographic region, and whether or not injection drug users (IDUs) played a significant role in given epidemic. Pooled ORs were stratified by prevalence level; very low-prevalence countries had an overall MSM OR of 58.4 (95% CI 56.3-60.6); low-prevalence countries, 14.4 (95% CI 13.8-14.9); and medium- to high-prevalence countries, 9.6 (95% CI 9.0-10.2). Significant differences in ORs for HIV infection among MSM in were seen when comparing low- and middle-income countries; low-income countries had an OR of 7.8 (95% CI 7.2-8.4), whereas middle-income countries had an OR of 23.4 (95% CI 22.8-24.0). Stratifying the pooled ORs by whether the country had a substantial component of IDU spread resulted in an OR of 12.8 (95% CI 12.3-13.4) in countries where IDU transmission was prevalent, and 24.4 (95% CI 23.7-25.2) where it was not. By region, the OR for MSM in the Americas was 33.3 (95% CI 32.3-34.2); 18.7 (95% CI 17.7-19.7) for Asia; 3.8 (95% CI 3.3-4.3) for Africa; and 1.3 (95% CI 1.1-1.6) for the low- and middle-income countries of Europe. CONCLUSIONS MSM have a markedly greater risk of being infected with HIV compared with general population samples from low- and middle-income countries in the Americas, Asia, and Africa. ORs for HIV infection in MSM are elevated across prevalence levels by country and decrease as general population prevalence increases, but remain 9-fold higher in medium-high prevalence settings. MSM from low- and middle-income countries are in urgent need of prevention and care, and appear to be both understudied and underserved.
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Affiliation(s)
- Stefan Baral
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Center for Public Health and Human Rights, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Department of Public Health Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Frangiscos Sifakis
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Center for Public Health and Human Rights, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Farley Cleghorn
- Constella Futures Group, Washington, D.C., United States of America
| | - Chris Beyrer
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Center for Public Health and Human Rights, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail:
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Locateli D, Stoco PH, de Queiroz ATL, Alcântara LCJ, Ferreira LGE, Zanetti CR, Rodrigues R, Grisard EC, Pinto AR. Molecular epidemiology of HIV-1 in Santa Catarina State confirms increases of subtype C in Southern Brazil. J Med Virol 2007; 79:1455-63. [PMID: 17705166 DOI: 10.1002/jmv.20955] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Recent studies have demonstrated an increased prevalence of human immunodeficiency virus type 1 (HIV-1) subtype C in southern Brazil. Although Santa Catarina State (SC) is located in this area and presents one of the country's highest incidences of HIV/AIDS, knowledge on the molecular epidemiology of HIV-1 in such State is lacking. The aim of this study was to investigate the HIV-1 molecular diversity and epidemiological profile of HIV-1-infected patients from SC. DNA samples were PCR amplified and HIV-1 subtypes were determined using both env and gag genes by direct sequencing. Phylogenetic analyses revealed that 48% were subtype C and 23% were subtype B. Possible recombinant forms were observed for both B/C (23%) and B/F (6%) subtypes. Our results, for the first time, identifies HIV-1 subtype C as a major clade circulating in SC and contributes to the understanding of HIV epidemics in the country by confirming the epidemic spread of the HIV-1 subtype C in southern Brazil.
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Affiliation(s)
- Dayse Locateli
- Laboratório de Imunologia Aplicada, Departamento de Microbiologia e Parasitologia, UFSC, Florianópolis, SC, Brazil
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Aulicino PC, Bello G, Rocco C, Romero H, Mangano A, Morgado MG, Sen L. Description of the first full-length HIV type 1 subtype F1 strain in Argentina: implications for the origin and dispersion of this subtype in South America. AIDS Res Hum Retroviruses 2007; 23:1176-82. [PMID: 17961101 DOI: 10.1089/aid.2007.0038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV-1 subtype F1 in South America is mainly found as part of diverse BF1 recombinant forms and only five full-length "pure" F1 strains from Brazil were characterized to date. In the present study we describe the first near full-length sequence of a nonrecombinant F1 HIV-1 strain from Argentina, and explore the epidemiological history of this subtype in South America. Three separate phylogenetic analyses were carried out: with all available F1 full-length sequences, with concatenated F1 sequences contained in F1 and BF1 strains, and with partial F1 env sequences derived from worldwide strains. All analyses were consistent in showing a local origin of the newly reported Argentine subtype F1 strain, and a common ancestry of the South American subtype F1 sequences, present either in pure or recombinant genomes. By coalescent analysis, the onset date of the HIV-1 subtype F1 epidemic in South America was estimated to be around the late 1970s. The results indicate for the first time that nonrecombinant F1 HIV-1 strains are present in Argentina, and suggest that the subtype F1 epidemic in South America was initiated by the introduction of a very small group of genetically related viruses during late 1970s.
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Affiliation(s)
- Paula C. Aulicino
- Laboratorio de Biología Celular y Retrovirus-CONICET, Hospital de Pediatría “J. P. Garrahan,” Buenos Aires, Argentina
| | - Gonzalo Bello
- Laboratory of AIDS and Molecular Immunology, Department of Immunology, Instituto Oswaldo Cruz–Fiocruz, Rio de Janeiro, Brazil
| | - Carlos Rocco
- Laboratorio de Biología Celular y Retrovirus-CONICET, Hospital de Pediatría “J. P. Garrahan,” Buenos Aires, Argentina
| | - Héctor Romero
- Laboratorio de Organización y Evolución del Genoma, Sección Biomatemáticas, Facultad de Ciencias, Universidad de la República, Uruguay
| | - Andrea Mangano
- Laboratorio de Biología Celular y Retrovirus-CONICET, Hospital de Pediatría “J. P. Garrahan,” Buenos Aires, Argentina
| | - Mariza G. Morgado
- Laboratory of AIDS and Molecular Immunology, Department of Immunology, Instituto Oswaldo Cruz–Fiocruz, Rio de Janeiro, Brazil
| | - Luisa Sen
- Laboratorio de Biología Celular y Retrovirus-CONICET, Hospital de Pediatría “J. P. Garrahan,” Buenos Aires, Argentina
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Stefani MMA, Pereira GAS, Lins JAB, Alcantara KC, Silveira AA, Viegas AA, Maya NC, Mussi AH. Molecular screening shows extensive HIV-1 genetic diversity in Central West Brazil. J Clin Virol 2007; 39:205-9. [PMID: 17537671 DOI: 10.1016/j.jcv.2007.04.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Revised: 04/11/2007] [Accepted: 04/14/2007] [Indexed: 12/01/2022]
Abstract
BACKGROUND Information is limited about HIV-1 subtypes circulating in less populated Brazilian areas where the AIDS epidemic is expanding, such as in the Central West region. OBJECTIVE To describe HIV-1 subtypes in patients from the States of Goias, Mato Grosso do Sul and Mato Grosso in Central West Brazil. STUDY DESIGN Heteroduplex mobility analysis of nested-PCR products from env (primers: ED5/ED12, ES7/ES8) and gag regions (primers: H1P202/H1G777, H1Gag1584/g17) of 406 HIV-1 isolates from Goias (n=271), Mato Grosso do Sul (n=85) and Mato Grosso (n=50) collected from 2001 to 2004. RESULTS Median age of patients was 26 years (1-79 range), 68.7% (279/406) females, 69.9% (269/385) sexual exposure, 14.3% parenteral risk, 15.8% vertical cases. Overall 69.9% (284/406) of HIV-1 subtypes were concordant B(env)/B(gag), 1.7% F(env)/F(gag) and 1% C(env)/C(gag). Discordant HIV-1 isolates were 14.5% (59/406), mainly B(env)/F(gag) and F(env)/B(gag) (49/59); five were B(env)/D(gag), four B(env)/C(gag) and one C(env)/D(gag). B/B and discordant B/F isolates were detected among all risk categories and among children and adults. CONCLUSION Extensive genetic diversity of HIV-1 was observed in Central West Brazil. Continued molecular studies should monitor the changing dynamics of HIV-1 over time especially in areas where the epidemic is growing.
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Affiliation(s)
- Mariane M A Stefani
- Tropical Pathology and Public Health Institute, Federal University of Goias, Rua Delenda Rezende de Melo s/n, Setor Universitario, 74.605-050 Goiania, Goias, Brazil.
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Distinguishing molecular forms of HIV-1 in Asia with a high-throughput, fluorescent genotyping assay, MHAbce v.2. Virology 2007; 358:178-91. [DOI: 10.1016/j.virol.2006.07.055] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2006] [Revised: 07/10/2006] [Accepted: 07/28/2006] [Indexed: 11/18/2022]
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Bautista CT, Sanchez JL, Montano SM, Laguna-Torres A, Suarez L, Sanchez J, Campos P, Gallardo C, Mosquera C, Villafane M, Aguayo N, Avila MM, Weissenbacher M, Ramirez E, Child R, Serra M, Aponte C, Mejia A, Velazques N, Gianella A, Perez J, Olson JG, Carr JK. Seroprevalence of and risk factors for HIV-1 infection among female commercial sex workers in South America. Sex Transm Infect 2006; 82:311-6. [PMID: 16877581 PMCID: PMC2564717 DOI: 10.1136/sti.2005.018234] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
OBJECTIVE Assessment of HIV prevalence and associated risk behaviours among female commercial sex workers (FCSW) across major cities in South America. METHODS Seroepidemiological, cross sectional studies of 13 600 FCSW were conducted in nine countries of South America during the years 1999-2002. Participants were recruited in brothels, massage parlours, hotels, and streets where anonymous questionnaires and blood samples were collected. HIV infection was determined by enzyme linked immunosorbent assay (ELISA) screening and western blot confirmatory tests. RESULTS The overall HIV seroprevalence was 1.2% (range 0.0%-4.5%). The highest HIV seroprevalences were reported in Argentina (4.5%) and Paraguay (2.6%); no HIV infected FCSW were detected in Venezuela and Chile. Consistent predictors of HIV seropositivity were: (1) a previous history of sexually transmitted infections (STI, AORs = 3.8-8.3), and (2) 10 years or more in commercial sex work (AORs = 2.2-24.8). In addition, multiple (> or =3) sexual contacts (AOR = 5.0), sex with foreigners (AOR = 6.9), use of illegal drugs (AOR = 3.2), and marijuana use (AOR = 8.2) were associated with HIV seropositivity in Southern Cone countries. CONCLUSIONS Consistently low HIV seroprevalences were detected among FCSW in South America, particularly in the Andean region. Predictors of HIV infection across the continent were STI and length of commercial sex work; however, use of illegal drugs, especially marijuana, and sexual contacts with foreigners were also found to be associated risk factors in the Southern Cone region. Interventions for the control of HIV and other STI need to be region and country specific; drug use appears to have an ever increasing role in the spread of HIV among heterosexually active populations.
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Affiliation(s)
- C T Bautista
- U.S. Military HIV Research Program at the Walter Reed Army Institute of Research, and the Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., 1 Taft Court, Suite 250, Rockville, MD 20850, USA.
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Eyzaguirre L, Bautista CT, Ayala C, Acosta J, Negrete M, Sateren WB, Montano SM, Sanchez JL, Carr JK. First case of HIV Type 1 subtype F among men who have sex with men in Colombia. AIDS Res Hum Retroviruses 2006; 22:808-11. [PMID: 16910838 DOI: 10.1089/aid.2006.22.808] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To study the molecular epidemiology of human immunodeficiency virus (HIV) strains among men who have sex with men (MSM), the main high-risk group for HIV infection in Colombia, 113 HIV-positive MSM subjects recruited in Bogotá during the year 2002 were genotyped. By heteroduplex mobility assay (env HMA) all samples were classified as subtype B. Partial sequencing of the protease and the reverse transcriptase (Pro/RT) regions performed on a random subset of 10 samples revealed that nine were classified as subtype B, and one sample was subtype F. The specimen that is subtype F in pol and subtype B in env is likely to be is either a recombinant or a dual infection. In this study, we identify the HIV F subtype for the first time in Colombia.
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Affiliation(s)
- Lindsay Eyzaguirre
- U.S. Military HIV Research Program at the Walter Reed Army Institute of Research, and the Henry M. Jackson Foundation for the Advancement Military Medicine, Inc., Rockville, Maryland 20850, USA
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Cáceres C, Konda K, Pecheny M, Chatterjee A, Lyerla R. Estimating the number of men who have sex with men in low and middle income countries. Sex Transm Infect 2006; 82 Suppl 3:iii3-9. [PMID: 16735290 PMCID: PMC2576725 DOI: 10.1136/sti.2005.019489] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
OBJECTIVES To collect and analyse published and unpublished surveillance and research data on the prevalence of same sex sexual activity among male adults (including male-to-female transgenders and sex workers) in low and middle income countries. METHODS Key indicators were operationalised (ever sex with a man, sex with a man last year, high risk sex last year (as defined by unprotected anal sex or commercial sex)) and a database was designed for data collection. Searches were conducted (PubMed, databases (US Census Bureau, World Bank, conferences)) and regional informants helped. Reference reports were used to assess the methodology and quality of information in each record. The best data available per region were identified and indicator estimates were used to propose regional range estimates. RESULTS Of 561 studies on male sexual behaviour and/or MSM population characteristics, 67 addressed prevalence of sex between men, with diverse numbers per region and virtual unavailability in sub-Saharan Africa, Middle East/North Africa, and the English speaking Caribbean. Overall, data on lifetime prevalence of sex with men (among males) yielded figures of 3-5% for East Asia, 6-12% for South and South East Asia, 6-15% for Eastern Europe, and 6-20% for Latin America. Last year figures were approximately half of lifetime figures, and prevalence of high risk sex among MSM last year was approximately 40-60% in all regions except South Asia, where it is 70-90%. CONCLUSIONS Data available on the prevalence of male same sex sexual activity across regions are scarce (non-existent in some areas), with validity and comparability problems. In South and South East Asia, Eastern Europe, and Latin America, a lifetime prevalence of 6-20% was estimated, with smaller figures in East Asia. A cross cultural analysis of terminology and practices is needed, as is continued work on epidemiological and social analysis of male-male sexual practices in societies across regions.
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Gutiérrez JP, Molina-Yepez D, Morrison K, Samuels F, Bertozzi SM. Correlates of condom use in a sample of MSM in Ecuador. BMC Public Health 2006; 6:152. [PMID: 16768794 PMCID: PMC1513207 DOI: 10.1186/1471-2458-6-152] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2005] [Accepted: 06/12/2006] [Indexed: 11/16/2022] Open
Abstract
Background In Ecuador, the prevalence of HIV in the general population is approximately 0.3%. However, up to 17% prevalence has been reported among specific groups of homosexual and bisexual men. The objective of this study is to explore correlates of condom use among men who have sex with men (MSM) across eight cities in Ecuador. Methods A cross-sectional survey design was used. A questionnaire including variables on sexual behaviour, demographics, and socio-economic characteristics was distributed to a sample of MSM in eight Ecuadorian cities. Results Information was obtained for 2,594 MSM across the eight cities. The largest subcategory of self-identification was active bisexuals (35%), followed by those who described themselves as "hombrados" (masculine gays, 22%). The mean age was 25 years, and the majority were unmarried (78%), with a median of 10 years of schooling (IQR 7 – 12). Regarding condom use, 55% of those interviewed had unprotected penetrative sex with each of their last three partners, and almost 25% had never used a condom. The most important correlates of condom use were single status, high life-skills rating, and high socio-economic status (RP 5.45, 95% CI 4.26 – 6.37; RP 1.84, 95% CI 1.79 – 1.86, and RP 1.20, 95% CI 1.01 – 1.31, respectively). Conclusion Our data illustrate the urgent need for targeted HIV-prevention programs for MSM populations in Ecuador. MSM have the highest HIV prevalence in the country, and condom use is extremely low. It is imperative that prevention strategies be re-evaluated and re-prioritized to more effectively respond to the Ecuadorian epidemic.
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Affiliation(s)
- Juan-Pablo Gutiérrez
- Division of Health Economics and Evaluation, National Institute of Public Health, Cuernavaca, Mexico
| | | | - Ken Morrison
- Division of Health Economics and Evaluation, National Institute of Public Health, Cuernavaca, Mexico
- POLICY Project, Mexico
| | - Fiona Samuels
- Research and Evaluation Unit, International HIV/AIDS Alliance, Brighton, UK
| | - Stefano M Bertozzi
- Division of Health Economics and Evaluation, National Institute of Public Health, Cuernavaca, Mexico
- Center for Economic Research and Education, A.C. (CIDE), México DF, Mexico
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Konings FAJ, Burda ST, Urbanski MM, Zhong P, Nadas A, Nyambi PN. Human immunodeficiency virus type 1 (HIV-1) circulating recombinant form 02_AG (CRF02_AG) has a higher in vitro replicative capacity than its parental subtypes A and G. J Med Virol 2006; 78:523-34. [PMID: 16555291 DOI: 10.1002/jmv.20572] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) circulating recombinant form (CRF) 02_AG is the predominant subtype in Cameroon, even more prevalent than the parental subtypes A and G. An important question that needs to be addressed is whether recombination in HIV-1 infection can lead to the emergence of viruses with biological advantages. The replicative capacity was investigated in peripheral blood mononuclear cells (PBMCs) of 13 R5-tropic primary HIV-1 isolates, including 5 CRF02_AG, 4 subtype A, and 4 subtype G viruses. HIV-1 subtype identity was defined by phylogeny either of the full-length genome or analysis of a combination of segments of the gag, pro, pol, and env genes followed by recombination breakpoint analysis. All viruses were grown on PBMCs for 11 days and culture supernatant was analyzed for reverse transcriptase (RT) activity and p24 production. On day 11 post-infection, CRF02_AG strains had a 1.4-1.9 times higher RT activity and reached a significantly higher level of p24 production than the parental subtypes A and G. Furthermore, the replication rate as measured by p24 production was 1.4 times higher for CRF02_AG strains compared to the subtypes A and G. This study suggests that the recombination event that led to CRF02_AG resulted in a variant with a better replicative capacity than its progenitors. This adaptation could contribute to the broader spread of HIV-1 CRF02_AG leading to its predominance in West Central Africa compared to the lower prevalence of its parental subtypes A and G.
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Affiliation(s)
- Frank A J Konings
- Department of Microbiology, New York University School of Medicine, New York, New York 10010, USA
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Sanabani S, Kleine Neto W, Kalmar EMN, Diaz RS, Janini LM, Sabino EC. Analysis of the near full length genomes of HIV-1 subtypes B, F and BF recombinant from a cohort of 14 patients in São Paulo, Brazil. INFECTION GENETICS AND EVOLUTION 2006; 6:368-77. [PMID: 16522378 DOI: 10.1016/j.meegid.2006.01.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2005] [Revised: 01/04/2006] [Accepted: 01/06/2006] [Indexed: 11/20/2022]
Abstract
The human immune deficiency virus (HIV) exhibits strikingly tremendous amount of genetic variability. Such feature is critically important for the virus to adapt to environmental changes by escaping the host immune system and by escaping candidate vaccine. Therefore, understanding of such diversity is fundamental for the design of successful drugs or vaccine, which is urgently needed to bring the HIV/AIDS epidemic under control. In this study, we investigated the magnitude of diversity of the HIV-1 near full-length genomes from patients previously assigned as infected with non-recombinant HIV-1 subtypes B and F1 variants based on small portion of viral genome. HIV-1 proviral DNA was extracted from 14 samples previously classified in our laboratory as six subtypes B and eight subtypes F on the basis of small amplicon sequencing. Reamplifications of DNA from these samples were carried out by an overlapping PCR followed by direct sequencing. The data were phylogenetically inferred. Sequence analysis revealed that two out of six partially identified subtype B and six out of eight partially identified subtype F were in fact BF recombinants throughout their full genomes. Two pairs BF recombinants had identical genomic recombination structure and distinct from the Argentinean CRF 12_BF strains, probably represents a novel circulating recombinant forms in Brazil. Our data provided new genetic material of some of the HIV-1 subtypes currently circulating in the country and points to the widespread of BF recombinants which are expected to change the epidemic nature by approaching the level of subtype B in Brazil.
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Kijak GH, McCutchan FE. HIV diversity, molecular epidemiology, and the role of recombination. Curr Infect Dis Rep 2005; 7:480-8. [PMID: 16225787 DOI: 10.1007/s11908-005-0051-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The magnitude of the HIV pandemic and its extensive genetic variation may earn it a unique place among infectious agents. A high mutation rate and a rampant recombination are driving HIV's evolution. Nine subtypes and a variety of recombinant forms of HIV now exist. The source of recombinant forms is the multiple infection of target cells, which becomes highly significant when individuals become infected with two or more divergent strains. In the current paper, we re-examine the role of dual infection and recombination in the generation of HIV-1 diversity, both in individuals and on a global scale. The current molecular epidemiology of HIV-1 is reviewed, emphasizing the latest reports from regional epidemics.
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Affiliation(s)
- Gustavo H Kijak
- US Military HIV Research Program, Henry M. Jackson Foundation, 1600 East Gude Drive, Rockville, MD 20850, USA.
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Montano SM, Sanchez JL, Laguna-Torres A, Cuchi P, Avila MM, Weissenbacher M, Serra M, Viñoles J, Russi JC, Aguayo N, Galeano AH, Gianella A, Andrade R, Arredondo A, Ramirez E, Acosta ME, Alava A, Montoya O, Guevara A, Manrique H, Sanchez JL, Lama JR, de la Hoz F, Sanchez GI, Ayala C, Pacheco ME, Carrion G, Chauca G, Perez JJ, Negrete M, Russell KL, Bautista CT, Olson JG, Watts DM, Birx DL, Carr JK. Prevalences, genotypes, and risk factors for HIV transmission in South America. J Acquir Immune Defic Syndr 2005; 40:57-64. [PMID: 16123683 DOI: 10.1097/01.qai.0000159667.72584.8b] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
HIV cross-sectional studies were conducted among high-risk populations in 9 countries of South America. Enzyme-linked immunosorbent assay screening and Western blot confirmatory testing were performed, and env heteroduplex mobility assay genotyping and DNA sequencing were performed on a subset of HIV-positive subjects. HIV prevalences were highest among men who have sex with men (MSM; 2.0%-27.8%) and were found to be associated with multiple partners, noninjection drug use (non-IDU), and sexually transmitted infections (STIs). By comparison, much lower prevalences were noted among female commercial sex workers (FCSWs; 0%-6.3%) and were associated mainly with a prior IDU and STI history. Env subtype B predominated among MSM throughout the region (more than 90% of strains), whereas env subtype F predominated among FCSWs in Argentina and male commercial sex workers in Uruguay (more than 50% of strains). A renewed effort in controlling STIs, especially among MSM groups, could significantly lessen the impact of the HIV epidemic in South America.
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Shepherd BE, Rossini AJ, Soto RJ, De Rivera IL, Mullins JI. Sampling designs for HIV molecular epidemiology with application to Honduras. AIDS Res Hum Retroviruses 2005; 21:907-14. [PMID: 16386105 DOI: 10.1089/aid.2005.21.907] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Proper sampling is essential to characterize the molecular epidemiology of human immunodeficiency virus (HIV). HIV sampling frames are difficult to identify, so most studies use convenience samples. We discuss statistically valid and feasible sampling techniques that overcome some of the potential for bias due to convenience sampling and ensure better representation of the study population. We employ a sampling design called stratified cluster sampling. This first divides the population into geographical and/or social strata. Within each stratum, a population of clusters is chosen from groups, locations, or facilities where HIV-positive individuals might be found. Some clusters are randomly selected within strata and individuals are randomly selected within clusters. Variation and cost help determine the number of clusters and the number of individuals within clusters that are to be sampled. We illustrate the approach through a study designed to survey the heterogeneity of subtype B strains in Honduras.
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Affiliation(s)
- Bryan E Shepherd
- Department of Biostastics, Medical Education, University of Washington, Seattle, Washington 98195-7232, USA.
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