Characterization of Human Immunodeficiency Virus type 1 (HIV-1) in a cohort of recently infected persons from the State of São Paulo by full genome sequencing

• Grant number: 06/50096-0
• Support type: Scholarships in Brazil - Post-Doctorate
• Effective date (Start): June 01, 2006
• Effective date (End): January 31, 2010
• Field of knowledge: Health Sciences - Medicine - Medical Clinics
• Principal researcher: Ricardo Sobhie Diaz
• Grantee: Sabri Saeed Mohammed Ahmed Al-Sanabani
• Home Institution: Escola Paulista de Medicina (EPM). Universidade Federal de São Paulo (UNIFESP). Campus São Paulo. São Paulo , SP, Brazil
• Associated research grant: 04/15856-9 - Prospective analysis of the virological and immunological characteristics in individuals with recent HIV-1 infection in the cities of São Paulo and Santos, AP.TEM

Abstract

The tremendous genetic variability of HIV has a direct impact on the development of molecular diagnostic tests and is a serious hurdle that confronts research in the development of a vaccine to counter the virus. It is therefore important to monitor the distribution and dynamics of HIV subtypes to avoid vaccination failure and a pitfall for molecular diagnostics The main objective of the current study is to characterize HIV-1 virtually full-length genome in a well-characterized cohort of individuals with recently acquired HIV-1 infection from the state of Sao Paulo. A total of EDTA-blood from 150 individuals with recently acquired HIV-1 infection on the bases of criteria established by other study will be enrolled. Amplification of proviral DNA from PBMC will be carried out by nested PCR according to the protocol established in our laboratory and supposes to result in 5 overlapping DNA fragments covering nearly full-length HIV-1 genome. Products will be sequenced and each sequence will be processed through phylogenetic analysis. Information on sequence alignment, evolution, cohort statistics, host genetic background, epitope mapping, clinical, immunological, and epidemiological data will be cross-referenced to viral sequences to allow for subsequent association studies (AU)

Scientific publications

(13)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

ALMEIDA, RAFAEL RIBEIRO; ROSA, DANIELA SANTORO; RIBEIRO, SUSAN PEREIRA; SANTANA, VINICIUS CANATO; KALLAS, ESPER GEORGES; SIDNEY, JOHN; SETTE, ALESSANDRO; KALIL, JORGE; CUNHA-NETO, EDECIO. Broad and Cross-Clade CD4(+) T-Cell Responses Elicited by a DNA Vaccine Encoding Highly Conserved and Promiscuous HIV-1 M-Group Consensus Peptides. PLoS One, v. 7, n. 9, SEP 18 2012. (04/15856-9, 06/50096-0, 08/57881-0)

SANABANI, SABRI SAEED; DE SOUZA PASTENA, EVELYN REGINA; KLEINE NETO, WALTER; BARRETO, CLAUDIA C.; FERRARI, KELLY T.; KALMAR, ERIKA M. N.; FERREIRA, SUZETE; SABINO, ESTER CERDEIRA. Near full-length genome analysis of low prevalent human immunodeficiency virus type 1 subclade F1 in Sao Paulo, Brazil. VIROLOGY JOURNAL, v. 6, JUN 16 2009. (06/50096-0)

SANABANI, SABRI SAEED; PESSOA, RODRIGO; SOARES DE OLIVEIRA, ANA CAROLINA; MARTINEZ, VANESSA POUZA; GIRET, MARIA TERESA MAIDANA; DE MENEZES SUCCI, REGINA CELIA; CARVALHO, KARINA; TOMIYAMA, CLAUDIA SATIKO; NIXON, DOUGLAS F.; SABINO, ESTER CERDEIRA; et al. Variability of HIV-1 Genomes among Children and Adolescents from Sao Paulo, Brazil. PLoS One, v. 8, n. 5, MAY 7 2013. (10/05845-0, 11/09983-1, 04/15856-9, 06/50096-0)

SANABANI‚ S.S.; PASTENA‚ ER; KLEINE NETO‚ W.; BARRETO‚ C.C.; FERRARI‚ K.T.; KALMAR‚ EM; FERREIRA‚ S.; SABINO‚ E.C.; OTHERS. Near full-length genome analysis of low prevalent human immunodeficiency virus type 1 subclade F1 in São Paulo‚ Brazil. VIROLOGY JOURNAL, v. 6, p. 78, 2009. (06/50096-0)

DUDLEY, DAWN M.; CHIN, EMILY N.; BIMBER, BENJAMIN N.; SANABANI, SABRI S.; TAROSSO, LEANDRO F.; COSTA, PRISCILLA R.; SAUER, MARIANA M.; KALLAS, ESPER G.; O'CONNOR, DAVID H.. Low-Cost Ultra-Wide Genotyping Using Roche/454 Pyrosequencing for Surveillance of HIV Drug Resistance. PLoS One, v. 7, n. 5, MAY 4 2012. (04/15856-9, 06/50096-0)

SANABANI‚ S.S.; PASTENA‚ ER; NETO‚ W.K.; MARTINEZ‚ V.P.; SABINO‚ E.C.; OTHERS. Characterization and frequency of a newly identified HIV-1 BF1 intersubtype circulating recombinant form in Sao Paulo‚ Brazil. VIROLOGY JOURNAL, v. 7, p. 74, 2010. (04/15856-9, 06/50096-0, 07/04890-0)

SANABANI‚ S.S.; DE SOUZA PASTENA‚ É.R.; DA COSTA‚ A.C.; MARTINEZ‚ V.P.; KLEINE-NETO‚ W.; DE OLIVEIRA‚ A.C.S.; SAUER‚ M.M.; BASSICHETTO‚ K.C.; OLIVEIRA‚ S.M.S.; TOMIYAMA‚ H.T.I.; et al. Characterization of partial and near full-length genomes of HIV-1 strains sampled from recently infected individuals in Sao Paulo‚ Brazil. PLoS One, v. 6, n. 10, p. e25869, 2011. (04/15856-9, 06/50096-0)

VINICIUS CANATO SANTANA; RAFAEL RIBEIRO ALMEIDA; SUSAN PEREIRA RIBEIRO; LUÍS CARLOS DE SOUZA FERREIRA; JORGE KALIL; DANIELA SANTORO ROSA; EDECIO CUNHA NETO. Co-administration of plasmid-encoded granulocyte-macrophage colony-stimulating factor increases human immunodeficiency virus-1 DNA vaccine-induced polyfunctional CD4+ T-cell responses. Memórias do Instituto Oswaldo Cruz, v. 110, n. 8, p. 1010-1016, 2015-11-24. (08/57881-0, 06/50096-0, 04/15856-9)

MAHNKE, YOLANDA D.; SONG, KAIMEI; SAUER, MARIANA M.; NASON, MARTHA C.; GIRET, MARIA TERESA M.; CARVALHO, KARINA I.; COSTA, PRISCILLA R.; ROEDERER, MARIO; KALLAS, ESPER G.. Early immunologic and virologic predictors of clinical HIV-1 disease progression. AIDS, v. 27, n. 5, p. 697-706, MAR 13 2013. (04/15856-9, 06/50096-0)

ALMEIDA, RAFAEL RIBEIRO; RAPOSO, RUI ANDRE SARAIVA; COIRADA, FERNANDA CAROLINE; DA SILVA, JAMILE RAMOS; DE SOUZA FERREIRA, LUIS CARLOS; KALIL, JORGE; NIXON, DOUGLAS F.; CUNHA-NETO, EDECIO. Modulating APOBEC expression enhances DNA vaccine immunogenicity. Immunology and Cell Biology, v. 93, n. 10, p. 868-876, NOV 2015. (04/15856-9, 06/50096-0, 08/57881-0)

SANTANA, VINICIUS CANATO; ALMEIDA, RAFAEL RIBEIRO; RIBEIRO, SUSAN PEREIRA; DE SOUZA FERREIRA, LIUS CARLOS; KALIL, JORGE; ROSA, DANIELA SANTORO; CUNHA-NETO, EDECIO. Co-administration of plasmid-encoded granulocyte-macrophage colony-stimulating factor increases human immunodeficiency virus-1 DNA vaccine-induced polyfunctional CD4(+) T-cell responses. Memórias do Instituto Oswaldo Cruz, v. 110, n. 8, p. 1010-1016, DEC 2015. (04/15856-9, 06/50096-0, 08/57881-0)

SANABANI, SABRI SAEED; DE SOUZA PASTENA, EVELYN REGINA; KLEINE NETO, WALTER; MARTINEZ, VANESSA POUZA; SABINO, ESTER CERDEIRA. Characterization and frequency of a newly identified HIV-1 BF1 intersubtype circulating recombinant form in Sao Paulo, Brazil. VIROLOGY JOURNAL, v. 7, APR 16 2010. (04/15856-9, 06/50096-0, 07/04890-0)

SANABANI, SABRI SAEED; DE SOUZA PASTENA, EVELYN REGINA; DA COSTA, ANTONIO CHARLYS; MARTINEZ, VANESSA POUZA; KLEINE-NETO, WALTER; SOARES DE OLIVEIRA, ANA CAROLINA; SAUER, MARIANA MELILLO; BASSICHETTO, KATIA CRISTINA; SANTOS OLIVEIRA, SOLANGE MARIA; IWASHITA TOMIYAMA, HELENA TOMOKO; et al. Characterization of Partial and Near Full-Length Genomes of HIV-1 Strains Sampled from Recently Infected Individuals in Sao Paulo, Brazil. PLoS One, v. 6, n. 10, OCT 14 2011. (04/15856-9, 06/50096-0)