title: Variability of HIV-1 genomes among children and adolescents from São Paulo, Brazil.
abstract: 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 Sao Paulo, Brazil.
  
  
  METHODS
  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.
authors.affiliation: Clinical and Research Laboratory (LIM 03), School of Medicine, University of São Paulo, São Paulo, Brazil. sabyem_63@yahoo.com
authors.forename: Sabri Saeed
authors.initials: SS
authors.lastname: Sanabani
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Pessôa
authors.forename: Ana Carolina
authors.initials: AC
authors.lastname: Soares de Oliveira
authors.forename: Vanessa Pouza
authors.initials: VP
authors.lastname: Martinez
authors.forename: Maria Teresa Maidana
authors.initials: MT
authors.lastname: Giret
authors.forename: Regina Célia
authors.initials: RC
authors.lastname: de Menezes Succi
authors.forename: Karina
authors.initials: K
authors.lastname: Carvalho
authors.forename: Claudia Satiko
authors.initials: CS
authors.lastname: Tomiyama
authors.forename: Douglas F
authors.initials: DF
authors.lastname: Nixon
authors.forename: Ester Cerdeira
authors.initials: EC
authors.lastname: Sabino
authors.forename: Esper Georges
authors.initials: EG
authors.lastname: Kallas
mesh_terms: D000293:Adolescent; D001938:Brazil; D002648:Child; D002675:Child, Preschool; D024882:Drug Resistance, Viral / Q000235:genetics; D005260:Female; D014644:Genetic Variation; D016679:Genome, Viral / Q000235:genetics*; D023281:Genomics; D005838:Genotype; D015497:HIV-1 / Q000187:drug effects / Q000235:genetics* / Q000502:physiology; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000378:metabolism; D008297:Male; D009154:Mutation; D056189:Viral Tropism / Q000235:genetics; D055815:Young Adult