title: Genetic characterization of HIV-1 BC recombinants and evolutionary history of the CRF31_BC in Southern Brazil.
abstract: To evaluate the recombination profiles and evolutionary history of HIV-1 BC recombinants in Southern Brazil, 81 isolates collected in the city of Porto Alegre (Rio Grande do Sul State) from 1998 to 2006 previously subtyped as C (env-gp120/C2V3) were screened in the protease-reverse transcriptase (pr/rt), integrase and gp41 genomic regions. Detailed phylogenetic, bootscan and informative site analyses were performed to trace the subtype classification. The evolutionary rate and divergence time of the Brazilian CRF31_BC epidemic were estimated using a Bayesian Markov Chain Monte Carlo framework. Analysis of the four target regions identified: 43 isolates as "pure" subtype C, 23 as CRF31_BC, and 15 as unique BC recombinant forms (URFs_BC). Recombination breakpoints were mainly localized in the rt gene and 100% of the recombinant samples could be detected analyzing only this region. Most URFs_BC (86.7%) contained small subtype B fragments (<or=160nt) in the rt region and shared one of the recombination breakpoints with CRF31_BC. In conclusion, despite the high co-prevalence of subtypes B and C in Porto Alegre, the diversity of BC recombinant forms circulating in this region was extremely low. Most BC recombinants were CRF31_BC and URFs_BC that appeared to be second generation recombinants derived from CRF31_BC and subtype C strains, confirming the importance of this CRF in this region. The emergence of the CRF31_BC was estimated to be around 1988 (1982-1992).
authors.affiliation: Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil.
authors.forename: Caroline Pereira Bittencourt
authors.initials: CP
authors.lastname: Passaes
authors.forename: Gonzalo
authors.initials: G
authors.lastname: Bello
authors.forename: Roberta S
authors.initials: RS
authors.lastname: Lorete
authors.forename: Sabrina E
authors.initials: SE
authors.lastname: Matos Almeida
authors.forename: Dennis Maletich
authors.initials: DM
authors.lastname: Junqueira
authors.forename: Valdilea G
authors.initials: VG
authors.lastname: Veloso
authors.forename: Mariza G
authors.initials: MG
authors.lastname: Morgado
authors.forename: Monick Lindenmeyer
authors.initials: ML
authors.lastname: Guimarães
mesh_terms: D001483:Base Sequence; D001499:Bayes Theorem; D001938:Brazil / Q000453:epidemiology; D019143:Evolution, Molecular; D015699:HIV Envelope Protein gp120 / Q000235:genetics; D015700:HIV Envelope Protein gp41 / Q000235:genetics; D015658:HIV Infections / Q000453:epidemiology / Q000821:virology; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D008390:Markov Chains; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D011995:Recombination, Genetic; D016415:Sequence Alignment; D054302:pol Gene Products, Human Immunodeficiency Virus / Q000235:genetics
chemical_list: D015699:HIV Envelope Protein gp120; D015700:HIV Envelope Protein gp41; D054302:pol Gene Products, Human Immunodeficiency Virus