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HIV quasispecies studies using ultra-deep sequencing

Grant number: 11/12156-0
Support type:Regular Research Grants
Duration: May 01, 2012 - December 31, 2014
Field of knowledge:Health Sciences - Medicine
Principal Investigator:Ricardo Sobhie Diaz
Grantee:Ricardo Sobhie Diaz
Home Institution: Escola Paulista de Medicina (EPM). Universidade Federal de São Paulo (UNIFESP). Campus São Paulo. São Paulo , SP, Brazil

Abstract

The low genetic diversity of HIV in patients diagnosed with recent infection is a consequence of genetic bottleneck during transmission. However, some studies demonstrated by Sanger sequencing that this event happens less frequently in female patients, suggesting that women have greater susceptibility to be primarily infected by multiple HIV variants. Hypothetically, HIV-infected women may have a greater risk to have been infected by drug-resistant variants. Transmitted drug-resistance has major impacts in the success of the antiretroviral therapy and, thus, in AIDS progression. Nevertheless, Sanger sequencing is not able to detect resistance variants present in less than 20% of the viral population. The present study aims to evaluate the hypothesis of women lacking genetic bottleneck during HIV-1 transmission using ultra-deep sequencing. Moreover, to estimate transmitted drug-resistance prevalence in patients newly-infected by HIV-1, also using ultra-deep sequencing. Twenty female and twenty male patients recently infected by HIV-1, not under antiretroviral therapy, will be evaluated. HIV-infected men and women will be paired to age, T CD4+ cells count and HIV-1 viral load. HIV-1 viral RNA and proviral DNA will be extracted from patients´ blood samples, the viral RNA reverse transcribed, and both viral cDNA and proviral DNA submitted to nested-PCR amplification of env and pol coding-regions. Next, the PCR products will be ultra-deep sequenced, followed by phylogenetic analysis. (AU)

Scientific publications (4)
(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)
DE CARVALHO LIMA, ELIDAMAR NUNES; ANDRADE LIMA, RODRIGO SUCUPIRA; CASTILHO PIQUEIRA, JOSE ROBERTO; CECILIA SUCUPIRA, MARIA; CAMARGO, MICHELLE; GALINSKAS, JULIANA; DIAZ, RICARDO SOBHIE. Evidence of genomic information and structural restrictions of HIV-1 PR and RT gene regions from individuals experiencing antiretroviral virologic failure. INFECTION GENETICS AND EVOLUTION, v. 78, MAR 2020. Web of Science Citations: 0.
LEDA, ANA RACHEL; HUNTER, JAMES; DE OLIVEIRA, URSULA CASTRO; DE AZEVEDO, INACIO JUNQUEIRA; KALLAS, ESPER G.; ARARIPE SUCUPIRA, MARIA CECILIA; DIAZ, RICARDO SOBHIE. HIV-1 genetic diversity and divergence and its correlation with disease progression among antiretroviral naive recently infected individuals. VIROLOGY, v. 541, p. 13-24, FEB 2020. Web of Science Citations: 0.
LEDA, ANA RACHEL; HUNTER, JAMES; OLIVEIRA, URSULA CASTRO; AZEVEDO, INACIO JUNQUEIRA; ARARIPE SUCUPIRA, MARIA CECILIA; DIAZ, RICARDO SOBHIE. Insights about minority HIV-1 strains in transmitted drug resistance mutation dynamics and disease progression. Journal of Antimicrobial Chemotherapy, v. 73, n. 7, p. 1930-1934, JUL 2018. Web of Science Citations: 0.
DE CARVALHO LIMA, ELIDAMAR NUNES; CASTILHO PIQUEIRA, JOSE ROBERTO; CAMARGO, MICHELLE; GALINSKAS, JULIANA; SUCUPIRA, MARIA CECILIA; DIAZ, RICARDO SOBHIE. Impact of antiretroviral resistance and virological failure on HIV-1 informational entropy. Journal of Antimicrobial Chemotherapy, v. 73, n. 4, p. 1054-1059, APR 2018. Web of Science Citations: 0.

Please report errors in scientific publications list by writing to: cdi@fapesp.br.