Characterization of Partial and Near Full-Length Genomes of HIV-1 Strains Sampled from Recently Infected Individuals in Sao Paulo, Brazil

Author(s):Show less -

Sanabani, Sabri Saeed ^{[1, 2, 3]} ; de Souza Pastena, Evelyn Regina ^[4] ; da Costa, Antonio Charlys ^{[4, 1]} ; Martinez, Vanessa Pouza ^[4] ; Kleine-Neto, Walter ^{[1, 3]} ; Soares de Oliveira, Ana Carolina ^{[4, 1]} ; Sauer, Mariana Melillo ^[2] ; Bassichetto, Katia Cristina ^[5] ; Santos Oliveira, Solange Maria ^[5] ; Iwashita Tomiyama, Helena Tomoko ^[2] ; Sabino, Ester Cerdeira ^{[4, 3]} ; Kallas, Esper Georges ^[2]

Affiliation

^[1] Univ Fed Sao Paulo, Dept Translat Med, Sao Paulo - Brazil

^[2] Univ Sao Paulo, Fac Med, Div Clin Immunol & Allergy, Sao Paulo - Brazil

^[3] Fundacao Pro Sangue, Blood Ctr Sau Paulo, Sao Paulo - Brazil

^[4] Univ Sao Paulo, Dept Infect Dis, Sao Paulo - Brazil

^[5] Publ Hlth Dept Sao Paulo, Sao Paulo - Brazil

• Document type: Journal article
• Source: PLoS One; v. 6, n. 10 OCT 14 2011.
• Web of Science Citations: 26

Abstract

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 Sao 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. (AU)

• FAPESP's process: 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
• Grantee: Ricardo Sobhie Diaz
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 06/50096-0 - 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
• Grantee: Sabri Saeed Mohammed Ahmed Al-Sanabani
• Support Opportunities: Scholarships in Brazil - Post-Doctoral