Variability of HIV-1 Genomes among Children and Adolescents from São Paulo, Brazil

Background: Genetic variability is a major feature of the human immunodeficiency virus type 1 (HIV-1) and considered the key factor to frustrating efforts to halt the virus epidemic. in this study, we aimed to investigate the genetic variability of HIV-1 strains among children and adolescents born from 1992 to 2009 in the state of São Paulo, Brazil.Methodology: Plasma and peripheral blood mononuclear cells (PBMC) were collected from 51 HIV-1-positive children and adolescents on ART followed between September 1992 and July 2009. After extraction, the genetic materials were used in a polymerase chain reaction (PCR) to amplify the viral near full length genomes (NFLGs) from 5 overlapped fragments. NFLGs and partial amplicons were directly sequenced and data were phylogenetically inferred.Results: of the 51 samples studied, the NFLGs and partial fragments of HIV-1 from 42 PBMCs and 25 plasma were successfully subtyped. Results based on proviral DNA revealed that 22 (52.4%) patients were infected with subtype B, 16 (38.1%) were infected with BF1 mosaic variants and 4 (9.5%) were infected with sub-subtype F1. All the BF1 recombinants were unique and distinct from any previously identified unique or circulating recombinant forms in South America. Evidence of dual infections was detected in 3 patients coinfected with the same or distinct HIV-1 subtypes. Ten of the 31 (32.2%) and 12 of the 21 (57.1%) subjects with recovered proviral and plasma, respectively, protease sequences were infected with major mutants resistant to protease inhibitors. the V3 sequences of 14 patients with available sequences from PBMC/or plasma were predicted to be R5-tropic virus except for two patients who harbored an X4 strain.Conclusions: the high proportion of HIV-1 BF1 recombinant, coinfection rate and vertical transmission in Brazil merits urgent attention and effective measures to reduce the transmission of HIV among spouses and sex partners.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)National Institutes of HealthUniv São Paulo, Sch Med, Clin & Res Lab LIM 03, São Paulo, BrazilUniv São Paulo, Inst Trop Med, Virol Lab LIM HCFMUSP 52, São Paulo, BrazilUniv Florida, Miller Sch Med, Story Lab 2, Miami, FL USAUniversidade Federal de São Paulo, Paulista Sch Med, Dept Pediat, São Paulo, BrazilUniv São Paulo, Sch Med, Div Clin Immunol & Allergy, São Paulo, BrazilUniv Calif San Francisco, Dept Med, Div Expt Med, San Francisco, CA USAUniversidade Federal de São Paulo, Paulista Sch Med, Dept Pediat, São Paulo, BrazilFAPESP: 2011/09983-1FAPESP: 2009/540055-5FAPESP: 2009/52381-2FAPESP: 2010/05845-0 2004/15856-9FAPESP: 2006/50096-0CAPES: 2571/2009National Institutes of Health: R01 AI060379Web of Scienc