Characterization of Partial and Near Full-Length Genomes of HIV-1 Strains Sampled from Recently Infected Individuals in São Paulo, Brazil
Autor(a) principal: | |
---|---|
Data de Publicação: | 2011 |
Outros Autores: | , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNIFESP |
Texto Completo: | http://repositorio.unifesp.br/handle/11600/34145 http://dx.doi.org/10.1371/journal.pone.0025869 |
Resumo: | Background: Genetic variability is a major feature of human immunodeficiency virus type 1 (HIV-1) and is considered the key factor frustrating efforts to halt the HIV epidemic. A proper understanding of HIV-1 genomic diversity is a fundamental prerequisite for proper epidemiology, genetic diagnosis, and successful drugs and vaccines design. Here, we report on the partial and near full-length genomic (NFLG) variability of HIV-1 isolates from a well-characterized cohort of recently infected patients in Sao Paul, Brazil.Methodology: HIV-1 proviral DNA was extracted from the peripheral blood mononuclear cells of 113 participants. the NFLG and partial fragments were determined by overlapping nested PCR and direct sequencing. the data were phylogenetically analyzed.Results: of the 113 samples (90.3% male; median age 31 years; 79.6% homosexual men) studied, 77 (68.1%) NFLGs and 32 (29.3%) partial fragments were successfully subtyped. of the successfully subtyped sequences, 88 (80.7%) were subtype B sequences, 12 (11%) BF1 recombinants, 3 (2.8%) subtype C sequences, 2 (1.8%) BC recombinants and subclade F1 each, 1 (0.9%) CRF02 AG, and 1 (0.9%) CRF31 BC. Primary drug resistance mutations were observed in 14/101 (13.9%) of samples, with 5.9% being resistant to protease inhibitors and nucleoside reverse transcriptase inhibitors (NRTI) and 4.9% resistant to non-NRTIs. Predictions of viral tropism were determined for 86 individuals. X4 or X4 dual or mixed-tropic viruses (X4/DM) were seen in 26 (30.2%) of subjects. the proportion of X4 viruses in homosexuals was detected in 19/69 (27.5%).Conclusions: Our results confirm the existence of various HIV-1 subtypes circulating in São Paulo, and indicate that subtype B account for the majority of infections. Antiretroviral (ARV) drug resistance is relatively common among recently infected patients. the proportion of X4 viruses in homosexuals was significantly higher than the proportion seen in other study populations. |
id |
UFSP_e8f462d55e53df4264bf204ec668093b |
---|---|
oai_identifier_str |
oai:repositorio.unifesp.br:11600/34145 |
network_acronym_str |
UFSP |
network_name_str |
Repositório Institucional da UNIFESP |
repository_id_str |
3465 |
spelling |
Sanabani, Sabri Saeed [UNIFESP]Souza Pastena, Evelyn Regina deCosta, Antonio Charlys da [UNIFESP]Martinez, Vanessa PouzaKleine-Neto, Walter [UNIFESP]Oliveira, Ana Carolina Soares de [UNIFESP]Sauer, Mariana MelilloBassichetto, Katia CristinaSantos Oliveira, Solange MariaTomiyama, Helena Tomoko IwashitaSabino, Ester CerdeiraKallas, Esper Georges [UNIFESP]Universidade de São Paulo (USP)Universidade Federal de São Paulo (UNIFESP)Fundacao Pro SanguePubl Hlth Dept São Paulo2016-01-24T14:17:19Z2016-01-24T14:17:19Z2011-10-14Plos One. San Francisco: Public Library Science, v. 6, n. 10, 11 p., 2011.1932-6203http://repositorio.unifesp.br/handle/11600/34145http://dx.doi.org/10.1371/journal.pone.0025869WOS000295981600017.pdf10.1371/journal.pone.0025869WOS:000295981600017Background: Genetic variability is a major feature of human immunodeficiency virus type 1 (HIV-1) and is considered the key factor frustrating efforts to halt the HIV epidemic. A proper understanding of HIV-1 genomic diversity is a fundamental prerequisite for proper epidemiology, genetic diagnosis, and successful drugs and vaccines design. Here, we report on the partial and near full-length genomic (NFLG) variability of HIV-1 isolates from a well-characterized cohort of recently infected patients in Sao Paul, Brazil.Methodology: HIV-1 proviral DNA was extracted from the peripheral blood mononuclear cells of 113 participants. the NFLG and partial fragments were determined by overlapping nested PCR and direct sequencing. the data were phylogenetically analyzed.Results: of the 113 samples (90.3% male; median age 31 years; 79.6% homosexual men) studied, 77 (68.1%) NFLGs and 32 (29.3%) partial fragments were successfully subtyped. of the successfully subtyped sequences, 88 (80.7%) were subtype B sequences, 12 (11%) BF1 recombinants, 3 (2.8%) subtype C sequences, 2 (1.8%) BC recombinants and subclade F1 each, 1 (0.9%) CRF02 AG, and 1 (0.9%) CRF31 BC. Primary drug resistance mutations were observed in 14/101 (13.9%) of samples, with 5.9% being resistant to protease inhibitors and nucleoside reverse transcriptase inhibitors (NRTI) and 4.9% resistant to non-NRTIs. Predictions of viral tropism were determined for 86 individuals. X4 or X4 dual or mixed-tropic viruses (X4/DM) were seen in 26 (30.2%) of subjects. the proportion of X4 viruses in homosexuals was detected in 19/69 (27.5%).Conclusions: Our results confirm the existence of various HIV-1 subtypes circulating in São Paulo, and indicate that subtype B account for the majority of infections. Antiretroviral (ARV) drug resistance is relatively common among recently infected patients. the proportion of X4 viruses in homosexuals was significantly higher than the proportion seen in other study populations.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Univ São Paulo, Fac Med, Div Clin Immunol & Allergy, São Paulo, BrazilUniversidade Federal de São Paulo, Dept Translat Med, São Paulo, BrazilFundacao Pro Sangue, Blood Ctr Sau Paulo, São Paulo, BrazilUniv São Paulo, Dept Infect Dis, São Paulo, BrazilPubl Hlth Dept São Paulo, São Paulo, BrazilUniversidade Federal de São Paulo, Dept Translat Med, São Paulo, BrazilFAPESP: 04/15856-9FAPESP: 2006/50096-0Web of Science11engPublic Library SciencePlos OneCharacterization of Partial and Near Full-Length Genomes of HIV-1 Strains Sampled from Recently Infected Individuals in São Paulo, Brazilinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da UNIFESPinstname:Universidade Federal de São Paulo (UNIFESP)instacron:UNIFESPORIGINALWOS000295981600017.pdfapplication/pdf1037674${dspace.ui.url}/bitstream/11600/34145/1/WOS000295981600017.pdf9a2b81cc782948c8cd8d2604a068cd2cMD51open accessTEXTWOS000295981600017.pdf.txtWOS000295981600017.pdf.txtExtracted texttext/plain47984${dspace.ui.url}/bitstream/11600/34145/2/WOS000295981600017.pdf.txtc8f0d3c691a17a5e1fbc1efae04e905dMD52open access11600/341452022-02-18 10:14:10.947open accessoai:repositorio.unifesp.br:11600/34145Repositório InstitucionalPUBhttp://www.repositorio.unifesp.br/oai/requestopendoar:34652022-02-18T13:14:10Repositório Institucional da UNIFESP - Universidade Federal de São Paulo (UNIFESP)false |
dc.title.en.fl_str_mv |
Characterization of Partial and Near Full-Length Genomes of HIV-1 Strains Sampled from Recently Infected Individuals in São Paulo, Brazil |
title |
Characterization of Partial and Near Full-Length Genomes of HIV-1 Strains Sampled from Recently Infected Individuals in São Paulo, Brazil |
spellingShingle |
Characterization of Partial and Near Full-Length Genomes of HIV-1 Strains Sampled from Recently Infected Individuals in São Paulo, Brazil Sanabani, Sabri Saeed [UNIFESP] |
title_short |
Characterization of Partial and Near Full-Length Genomes of HIV-1 Strains Sampled from Recently Infected Individuals in São Paulo, Brazil |
title_full |
Characterization of Partial and Near Full-Length Genomes of HIV-1 Strains Sampled from Recently Infected Individuals in São Paulo, Brazil |
title_fullStr |
Characterization of Partial and Near Full-Length Genomes of HIV-1 Strains Sampled from Recently Infected Individuals in São Paulo, Brazil |
title_full_unstemmed |
Characterization of Partial and Near Full-Length Genomes of HIV-1 Strains Sampled from Recently Infected Individuals in São Paulo, Brazil |
title_sort |
Characterization of Partial and Near Full-Length Genomes of HIV-1 Strains Sampled from Recently Infected Individuals in São Paulo, Brazil |
author |
Sanabani, Sabri Saeed [UNIFESP] |
author_facet |
Sanabani, Sabri Saeed [UNIFESP] Souza Pastena, Evelyn Regina de Costa, Antonio Charlys da [UNIFESP] Martinez, Vanessa Pouza Kleine-Neto, Walter [UNIFESP] Oliveira, Ana Carolina Soares de [UNIFESP] Sauer, Mariana Melillo Bassichetto, Katia Cristina Santos Oliveira, Solange Maria Tomiyama, Helena Tomoko Iwashita Sabino, Ester Cerdeira Kallas, Esper Georges [UNIFESP] |
author_role |
author |
author2 |
Souza Pastena, Evelyn Regina de Costa, Antonio Charlys da [UNIFESP] Martinez, Vanessa Pouza Kleine-Neto, Walter [UNIFESP] Oliveira, Ana Carolina Soares de [UNIFESP] Sauer, Mariana Melillo Bassichetto, Katia Cristina Santos Oliveira, Solange Maria Tomiyama, Helena Tomoko Iwashita Sabino, Ester Cerdeira Kallas, Esper Georges [UNIFESP] |
author2_role |
author author author author author author author author author author author |
dc.contributor.institution.none.fl_str_mv |
Universidade de São Paulo (USP) Universidade Federal de São Paulo (UNIFESP) Fundacao Pro Sangue Publ Hlth Dept São Paulo |
dc.contributor.author.fl_str_mv |
Sanabani, Sabri Saeed [UNIFESP] Souza Pastena, Evelyn Regina de Costa, Antonio Charlys da [UNIFESP] Martinez, Vanessa Pouza Kleine-Neto, Walter [UNIFESP] Oliveira, Ana Carolina Soares de [UNIFESP] Sauer, Mariana Melillo Bassichetto, Katia Cristina Santos Oliveira, Solange Maria Tomiyama, Helena Tomoko Iwashita Sabino, Ester Cerdeira Kallas, Esper Georges [UNIFESP] |
description |
Background: Genetic variability is a major feature of human immunodeficiency virus type 1 (HIV-1) and is considered the key factor frustrating efforts to halt the HIV epidemic. A proper understanding of HIV-1 genomic diversity is a fundamental prerequisite for proper epidemiology, genetic diagnosis, and successful drugs and vaccines design. Here, we report on the partial and near full-length genomic (NFLG) variability of HIV-1 isolates from a well-characterized cohort of recently infected patients in Sao Paul, Brazil.Methodology: HIV-1 proviral DNA was extracted from the peripheral blood mononuclear cells of 113 participants. the NFLG and partial fragments were determined by overlapping nested PCR and direct sequencing. the data were phylogenetically analyzed.Results: of the 113 samples (90.3% male; median age 31 years; 79.6% homosexual men) studied, 77 (68.1%) NFLGs and 32 (29.3%) partial fragments were successfully subtyped. of the successfully subtyped sequences, 88 (80.7%) were subtype B sequences, 12 (11%) BF1 recombinants, 3 (2.8%) subtype C sequences, 2 (1.8%) BC recombinants and subclade F1 each, 1 (0.9%) CRF02 AG, and 1 (0.9%) CRF31 BC. Primary drug resistance mutations were observed in 14/101 (13.9%) of samples, with 5.9% being resistant to protease inhibitors and nucleoside reverse transcriptase inhibitors (NRTI) and 4.9% resistant to non-NRTIs. Predictions of viral tropism were determined for 86 individuals. X4 or X4 dual or mixed-tropic viruses (X4/DM) were seen in 26 (30.2%) of subjects. the proportion of X4 viruses in homosexuals was detected in 19/69 (27.5%).Conclusions: Our results confirm the existence of various HIV-1 subtypes circulating in São Paulo, and indicate that subtype B account for the majority of infections. Antiretroviral (ARV) drug resistance is relatively common among recently infected patients. the proportion of X4 viruses in homosexuals was significantly higher than the proportion seen in other study populations. |
publishDate |
2011 |
dc.date.issued.fl_str_mv |
2011-10-14 |
dc.date.accessioned.fl_str_mv |
2016-01-24T14:17:19Z |
dc.date.available.fl_str_mv |
2016-01-24T14:17:19Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.citation.fl_str_mv |
Plos One. San Francisco: Public Library Science, v. 6, n. 10, 11 p., 2011. |
dc.identifier.uri.fl_str_mv |
http://repositorio.unifesp.br/handle/11600/34145 http://dx.doi.org/10.1371/journal.pone.0025869 |
dc.identifier.issn.none.fl_str_mv |
1932-6203 |
dc.identifier.file.none.fl_str_mv |
WOS000295981600017.pdf |
dc.identifier.doi.none.fl_str_mv |
10.1371/journal.pone.0025869 |
dc.identifier.wos.none.fl_str_mv |
WOS:000295981600017 |
identifier_str_mv |
Plos One. San Francisco: Public Library Science, v. 6, n. 10, 11 p., 2011. 1932-6203 WOS000295981600017.pdf 10.1371/journal.pone.0025869 WOS:000295981600017 |
url |
http://repositorio.unifesp.br/handle/11600/34145 http://dx.doi.org/10.1371/journal.pone.0025869 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.ispartof.none.fl_str_mv |
Plos One |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
11 |
dc.publisher.none.fl_str_mv |
Public Library Science |
publisher.none.fl_str_mv |
Public Library Science |
dc.source.none.fl_str_mv |
reponame:Repositório Institucional da UNIFESP instname:Universidade Federal de São Paulo (UNIFESP) instacron:UNIFESP |
instname_str |
Universidade Federal de São Paulo (UNIFESP) |
instacron_str |
UNIFESP |
institution |
UNIFESP |
reponame_str |
Repositório Institucional da UNIFESP |
collection |
Repositório Institucional da UNIFESP |
bitstream.url.fl_str_mv |
${dspace.ui.url}/bitstream/11600/34145/1/WOS000295981600017.pdf ${dspace.ui.url}/bitstream/11600/34145/2/WOS000295981600017.pdf.txt |
bitstream.checksum.fl_str_mv |
9a2b81cc782948c8cd8d2604a068cd2c c8f0d3c691a17a5e1fbc1efae04e905d |
bitstream.checksumAlgorithm.fl_str_mv |
MD5 MD5 |
repository.name.fl_str_mv |
Repositório Institucional da UNIFESP - Universidade Federal de São Paulo (UNIFESP) |
repository.mail.fl_str_mv |
|
_version_ |
1802764108708184064 |