title: The detection of in vivo and in vitro HIV type 1 B/F profiles in Brazil using a real-time PCR assay for five HIV type 1 genomic regions.
abstract: We sought to determine the frequency and profile of HIV-1 BF recombinants in vitro and in vivo. Laboratory HIV-1 strains from subtypes B and F were cocultured and evaluated. Clinical samples from the city of Santos, Brazil, where the first HIV-1 B/F circulating recombinant forms (CRF) were described, were also assessed. Five real-time PCR assays were developed to equally amplify subtypes B and F, and subtype-specific probes were developed and optimized. To validate the PCR systems, clinical samples from Santos were sequenced and phylogenetically analyzed. The real-time PCR assays were performed on these samples and on the supernatant of an in vitro competition assay to assess emergent recombinant strains. Out of 157 clinical samples, 62.1% were defined as subtype B, 3.0% were subtype F, 16.7% presented the CRF28_BF profile, and 13.6% of the samples presented the CRF29_BF profile. The specificity and sensitivity in the discrimination assay for this sample panel were 93% and 92%, respectively. The HIV that emerged from the coinfected cell culture closely resembled the CRF28_BF profile. The first-described CRFs are still fixed in this geographic region of Brazil, and the in vitro emerging strains detected by real-time PCR suggest that in addition to the shaping of recombinant strains by immune selection, viral structures may also play an important role in emerging CRFs.
authors: Retrovirology Laboratory, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil.
authors: Daniela
authors: D
authors: Teixeira
authors: Patricia
authors: P
authors: Munerato
authors: Shirley Cavalcante Vasconcelos
authors: SC
authors: Komninakis
authors: Erika Etsuko
authors: EE
authors: Fusuma
authors: Luiz Mario
authors: LM
authors: Janini
authors: Maria Cecilia Araripe
authors: MC
authors: Sucupira
authors: Ricardo Sobhie
authors: RS
authors: Diaz
mesh_terms: D001938:Brazil / Q000453:epidemiology; D002460:Cell Line; D016679:Genome, Viral; D015658:HIV Infections / Q000453:epidemiology*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012367:RNA, Viral / Q000235:genetics; D012680:Sensitivity and Specificity; D017423:Sequence Analysis, RNA
chemical_list: D012367:RNA, Viral