Complete genomes for HIV: viral genetic diversity among seropositive first-time blood donors in four blood centres in Brazil

• Grant number: 11/11090-5
• Support Opportunities: Regular Research Grants
• Start date: October 01, 2011
• End date: March 31, 2014
• Field of knowledge: Health Sciences - Medicine - Medical Clinics
• Principal Investigator: Sabri Saeed Mohammed Ahmed Al-Sanabani
• Grantee: Sabri Saeed Mohammed Ahmed Al-Sanabani
• Host Institution: Instituto de Medicina Tropical de São Paulo (IMT). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated researchers: Antonio Charlys da Costa ; Esper Georges Kallás ; Ester Cerdeira Sabino ; João Eduardo Ferreira ; Walter Kleine Neto

Abstract

The extraordinary genetic variability of HIV-1 posed particular challenge to diagnostic, monitoring and treatment, and it is the main hurdle for the development of an effective AIDS vaccine. In this study, we aim to analyse the complete viral genomes from 300 HIV-1 infected blood donors living in Rio de Janeiro (n=90), Sao Paulo (n=70), Minas Gerais (n=50) and Pernambuco state (n=90). These data will allow us to optimize strategies for HIV-1 diagnosis, to identify important signatures and polymorphisms throughout sequenced fragments and their association with the biological evolution of CD4 T cell counts or plasma viremia, to provide an estimate of cross clade conservation of the best-defined HIV-1 cytotoxic T-lymphocyte (CTL) epitopes by comparing the predicted protein sequences of our isolates to the reference optimal epitope sequences from a large number of HLA class 1 and II alleles covering more than 90% of HLA haplotypes in different populations, to define the structural pattern of recombinant strains, if exist, and determine their proportions, provide more HIV-1 Brazilian sequences characterized on more than one region of the genomes from different areas, which are still rare in HIV database, to describe the classification stability of HIV-1 subtypes at the level of full genomes since most available studies to date have reported only the assessment of partial genomes and to screen the entire viral genomes for resistance to available drug therapies. Furthermore, studying the phylogenetic clustering of these sequences, we will allow us to identify and characterize chains of transmission of HIV-1 isolates between different transmission groups. Finally, gaining such information may also prove valuable in developments of future vaccine that target speci c viral strains. To generates these sequences, HIV-1 plasma RNA from from all recruited patients will be extracted amplified by nested polymerase chain reactions (PCR) from five overlapped fragments according to our established methods. Amplified products will be purified and directly sequenced on both strands. All sequenced fragments will be edited, assembled and analyzed by different phylogentic and other appropriate tools. Information on evolution, cohort statistics, host genetic background, epitope mapping, clinical, and epidemiological data will be cross-referenced to viral sequences to allow for subsequent association studies. (AU)

Scientific publications

(8)

(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)

PESSOA, RODRIGO; LOUREIRO, PAULA; LOPES, MARIA ESTHER; CARNEIRO-PROIETTI, ANNA B. F.; SABINO, ESTER C.; BUSCH, MICHAEL P.; SANABANI, SABRI S.. Ultra-Deep Sequencing of HIV-1 near Full-Length and Partial Proviral Genomes Reveals High Genetic Diversity among Brazilian Blood Donors. PLoS One, v. 11, n. 3, MAR 31 2016. (11/11090-5, 14/24596-2, 11/12297-2)

PESSOA, RODRIGO; SABINO, ESTER C.; SANABANI, SABRI S.. Frequency of coreceptor tropism in PBMC samples from HIV-1 recently infected blood donors by massively parallel sequencing: the REDS II study. VIROLOGY JOURNAL, v. 12, MAY 14 2015. (11/11090-5, 14/24596-2, 11/12297-2)

PESSOA, RODRIGO; LOPES, MARIA ESTHER; SANABANI, SABRI S.. Genetic Characterization of HIV-1 Subtype D Near-Full-Length Proviral Genomes by Illumina Massively Parallel Sequencing Technology. GENOME ANNOUNCEMENTS, v. 2, n. 3, p. 2-pg., 2014-05-01. (11/12297-2, 11/11090-5)

PEREIRA DA FONSECA, TAIRACAN AUGUSTO; PESSOA, RODRIGO; SANABANI, SABRI SAEED. Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH, v. 12, n. 10, p. 13276-13288, OCT 2015. (11/11090-5, 11/12297-2)

PESSOA, RODRIGO; SANABANI, SABRI S.. Frequent detection of CXCR4-using viruses among Brazilian blood donors with HIV-1 long-standing infection and unknown clinical stage: Analysis of massive parallel sequencing data. DATA IN BRIEF, v. 6, p. 267-274, MAR 2016. (14/24596-2, 11/12297-2, 11/11090-5)

PESSOA, RODRIGO; WATANABE, JAQUELINE TOMOKO; CALABRIA, PAULA; FELIX, ALVINA CLARA; LOUREIRO, PAULA; SABINO, ESTER C.; BUSCH, MICHAEL P.; SANABANI, SABRI S.; RECIPIENT, INT COMPONENT NHLBI. Deep Sequencing of HIV-1 near Full-Length Proviral Genomes Identifies High Rates of BF1 Recombinants Including Two Novel Circulating Recombinant Forms (CRF) 70_BF1 and a Disseminating 71_BF1 among Blood Donors in Pernambuco, Brazil. PLoS One, v. 9, n. 11, NOV 17 2014. (11/11090-5, 11/12297-2)

PESSOA, RODRIGO; WATANABE, JAQUELINE TOMOKO; CALABRIA, PAULA; ALENCAR, CECILIA SALETE; LOUREIRO, PAULA; LOPES, MARIA ESTHER; PROETTI, ANNA BARBARA; FELIX, ALVINA CLARA; SABINO, ESTER C.; BUSCH, MICHAEL P.; et al. Enhanced detection of viral diversity using partial and near full-length genomes of human immunodeficiency virus Type 1 provirus deep sequencing data from recently infected donors at four blood centers in Brazil. Transfusion, v. 55, n. 5, p. 980-990, MAY 2015. (11/11090-5, 11/12297-2)

PESSOA, RODRIGO; DE FREITAS CARNEIRO PROIETTI, ANNA BRBARA; BUSCH, MICHAEL P.; SANABANI, SABRI S.. Identification of a Novel HIV-1 Circulating Recombinant Form (CRF72_BF1) in Deep Sequencing Data from Blood Donors in Southeastern Brazil. GENOME ANNOUNCEMENTS, v. 2, n. 3, p. 2-pg., 2014-05-01. (11/12297-2, 11/11090-5)