Estimating HIV-1 Genetic Diversity in Brazil Through Next-Generation Sequencing
Approximately 36.7 million people were living with the human immunodeficiency virus (HIV) at the end of 2016 according to UNAIDS, representing a global prevalence rate of 0.8%. In Brazil, an HIV prevalence of 0.24% has been estimated, which represents approximately 830,000 individuals living with th...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-04-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2019.00749/full |
| _version_ | 1818525703735345152 |
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| author | Brunna M. Alves Juliana D. Siqueira Isabel M. Prellwitz Ornella M. Botelho Vanusa P. Da Hora Sabri Sanabani Patrícia Recordon-Pinson Hervé Fleury Esmeralda A. Soares Marcelo A. Soares Marcelo A. Soares |
| author_facet | Brunna M. Alves Juliana D. Siqueira Isabel M. Prellwitz Ornella M. Botelho Vanusa P. Da Hora Sabri Sanabani Patrícia Recordon-Pinson Hervé Fleury Esmeralda A. Soares Marcelo A. Soares Marcelo A. Soares |
| author_sort | Brunna M. Alves |
| collection | DOAJ |
| description | Approximately 36.7 million people were living with the human immunodeficiency virus (HIV) at the end of 2016 according to UNAIDS, representing a global prevalence rate of 0.8%. In Brazil, an HIV prevalence of 0.24% has been estimated, which represents approximately 830,000 individuals living with the virus. As a touristic and commercial hub in Latin America, Brazil harbors an elevated HIV genetic variability, further contributed by the selective pressure exerted by the host immune system and by antiretroviral treatment. Through the progress of the next-generation sequencing (NGS) techniques, it has been possible to expand the study of HIV genetic diversity, evolutionary, and epidemic processes, allowing the generation of HIV complete or near full-length genomes (NFLG) and improving the characterization of intra- and interhost diversity of viral populations. Greater sensitivity in the detection of viral recombinant forms represents one of the major improvements associated with this development. It is possible to identify unique or circulating recombinant forms using the near full-length viral genomes with increasing accuracy. It also permits the characterization of multiple viral infections within individual hosts. Previous Brazilian studies using NGS to analyze HIV diversity were able to identify several distinct unique and circulating recombinant forms and evidenced dual infections. These data unveiled unprecedented high rates of viral recombination and highlighted that novel recombinants are continually arising in the Brazilian epidemic. In the pooled analysis depicted in this report, HIV subtypes have been determined from HIV-positive patients in five states of Brazil with some of the highest HIV prevalence, three in the Southeast (Rio de Janeiro, São Paulo, and Minas Gerais), one in the Northeast (Pernambuco) and one in the South (Rio Grande do Sul). Combined data analysis showed a significant prevalence of recombinant forms (29%; 101/350), and a similar 26% when only NFLGs were considered. Moreover, the analysis was able to evidence the occurrence of multiple infections in some individuals. Our data highlight the great HIV genetic diversity found in Brazil and unveils a more accurate scenario of the HIV evolutionary dynamics in the region. |
| first_indexed | 2024-12-11T06:12:32Z |
| format | Article |
| id | doaj.art-818d60f2a6904ff6b8e9d885864eed65 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-11T06:12:32Z |
| publishDate | 2019-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-818d60f2a6904ff6b8e9d885864eed652022-12-22T01:18:04ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2019-04-011010.3389/fmicb.2019.00749430811Estimating HIV-1 Genetic Diversity in Brazil Through Next-Generation SequencingBrunna M. Alves0Juliana D. Siqueira1Isabel M. Prellwitz2Ornella M. Botelho3Vanusa P. Da Hora4Sabri Sanabani5Patrícia Recordon-Pinson6Hervé Fleury7Esmeralda A. Soares8Marcelo A. Soares9Marcelo A. Soares10Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, BrazilPrograma de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, BrazilPrograma de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, BrazilPrograma de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, BrazilLaboratório de Biologia Molecular, Escola de Medicina, Universidade Federal do Rio Grande, Rio Grande do Sul, BrazilLIM-3, Hospital das Clinicas FMUSP, Faculty of Medicine, University of São Paulo, São Paulo, BrazilCNRS MFP-UMR 5234, University Hospital of Bordeaux, University of Bordeaux, Bordeaux, FranceCNRS MFP-UMR 5234, University Hospital of Bordeaux, University of Bordeaux, Bordeaux, FrancePrograma de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, BrazilPrograma de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, BrazilDepartamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, BrazilApproximately 36.7 million people were living with the human immunodeficiency virus (HIV) at the end of 2016 according to UNAIDS, representing a global prevalence rate of 0.8%. In Brazil, an HIV prevalence of 0.24% has been estimated, which represents approximately 830,000 individuals living with the virus. As a touristic and commercial hub in Latin America, Brazil harbors an elevated HIV genetic variability, further contributed by the selective pressure exerted by the host immune system and by antiretroviral treatment. Through the progress of the next-generation sequencing (NGS) techniques, it has been possible to expand the study of HIV genetic diversity, evolutionary, and epidemic processes, allowing the generation of HIV complete or near full-length genomes (NFLG) and improving the characterization of intra- and interhost diversity of viral populations. Greater sensitivity in the detection of viral recombinant forms represents one of the major improvements associated with this development. It is possible to identify unique or circulating recombinant forms using the near full-length viral genomes with increasing accuracy. It also permits the characterization of multiple viral infections within individual hosts. Previous Brazilian studies using NGS to analyze HIV diversity were able to identify several distinct unique and circulating recombinant forms and evidenced dual infections. These data unveiled unprecedented high rates of viral recombination and highlighted that novel recombinants are continually arising in the Brazilian epidemic. In the pooled analysis depicted in this report, HIV subtypes have been determined from HIV-positive patients in five states of Brazil with some of the highest HIV prevalence, three in the Southeast (Rio de Janeiro, São Paulo, and Minas Gerais), one in the Northeast (Pernambuco) and one in the South (Rio Grande do Sul). Combined data analysis showed a significant prevalence of recombinant forms (29%; 101/350), and a similar 26% when only NFLGs were considered. Moreover, the analysis was able to evidence the occurrence of multiple infections in some individuals. Our data highlight the great HIV genetic diversity found in Brazil and unveils a more accurate scenario of the HIV evolutionary dynamics in the region.https://www.frontiersin.org/article/10.3389/fmicb.2019.00749/fullHIV-1genetic diversityNGSNFLGsubtype |
| spellingShingle | Brunna M. Alves Juliana D. Siqueira Isabel M. Prellwitz Ornella M. Botelho Vanusa P. Da Hora Sabri Sanabani Patrícia Recordon-Pinson Hervé Fleury Esmeralda A. Soares Marcelo A. Soares Marcelo A. Soares Estimating HIV-1 Genetic Diversity in Brazil Through Next-Generation Sequencing Frontiers in Microbiology HIV-1 genetic diversity NGS NFLG subtype |
| title | Estimating HIV-1 Genetic Diversity in Brazil Through Next-Generation Sequencing |
| title_full | Estimating HIV-1 Genetic Diversity in Brazil Through Next-Generation Sequencing |
| title_fullStr | Estimating HIV-1 Genetic Diversity in Brazil Through Next-Generation Sequencing |
| title_full_unstemmed | Estimating HIV-1 Genetic Diversity in Brazil Through Next-Generation Sequencing |
| title_short | Estimating HIV-1 Genetic Diversity in Brazil Through Next-Generation Sequencing |
| title_sort | estimating hiv 1 genetic diversity in brazil through next generation sequencing |
| topic | HIV-1 genetic diversity NGS NFLG subtype |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2019.00749/full |
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