Analysis of HIV-1 BF pr/rt recombinant strains from Rio de Janeiro/Brazil reveals multiple unrelated mosaic structures.

Due to the co-circulation of HIV-1 subtypes B and F1 in Brazil, a large variety of unique BF1 recombinant forms (URFs_BF1) and four circulating BF1 recombinant forms (CRF28, CRF29, CRF39 and CRF40) have been described. The aim of this study was to investigate mosaic structure and phylogenetic relationship among several BF1 (protease-reverse transcriptase, pr/rt) recombinant sequences obtained from a group of patients from Rio de Janeiro, Brazil, from 1994 to 2005. Phylogenetic relationships were estimated by Bayesian and SplitsTree methods. Recombination breakpoints were analyzed by Bootscan. Those samples presenting the same recombinant pattern in the pr/rt region were investigated in the integrase (int) and envelope (env) regions as a screening method for the detection of potential new CRFs candidates. Third out of 61 pr/rt HIV-1 BF1 recombinant sequences analyzed depicted unique recombinant structures and were classified URFs_BF1. The other 31 samples segregated in eight well-supported phylogenetic clusters composed of at least three samples sharing the same recombination pattern. Analyses of the int and env regions from these 31 samples revealed that 11 samples were URFs_BF1. Three and four sequences corresponded, respectively, to the previously described CRF39 and CRF40. Three samples displayed a CRF28-like mosaic structure, and one sample a CRF29-like mosaic pattern. The other nine BF1 samples segregate in three distinct clusters with the same recombination profile and could represent good candidates for new CRFs_BF profiles. The HIV-1 BF1 epidemic in Rio de Janeiro is characterized by a high prevalence (67%) of URFs_BF1 and a low prevalence (4.9-6.6%) of each CRFs_BF previously identified in Brazil.

Guimarães ML ，Couto-Fernandez JC ，Eyer-Silva Wde A ，Teixeira SL ，Chequer-Fernandez SL ，Morgado MG ... -  《-》

Longitudinal analysis of HIV-1 BF1 recombinant strains in vertically infected children from Argentina reveals a decrease in CRF12_BF pol gene mosaic patterns and high diversity of BF unique recombinant forms.

The HIV-1 epidemic associated to BF1 recombinants in South America is both complex and intriguing, with an underestimated diversity of recombinant structures. Our aim was to explore the characteristics and temporal dynamics of the HIV-1 BF1 epidemic in Argentina, through the study of 172 HIV-1 pol BF1 recombinant sequences obtained from HIV-1 vertically infected patients born from 1986 to 2008. Recombination patterns were characterized by bootscanning, subtype signature analysis, and phylogenetic approaches. Proportion of sequences sharing common ancestry and recombination breakpoints with the Circulating Recombinant Form (CRF) CRF12_BF was compared against sequences with a non-CRF12_BF pattern in three study periods, and by fitting the data to a logistic model. Twenty-eight HIV-1 pol BF1 mosaic structures were identified, including four of the seven South-American CRF_BF-like patterns. However, common ancestry of these sequences with reference CRF strains only confirmed the presence of CRF12_BF (51.1%) and CRF17_BF (1.2%) among the Argentine BF pol sequences. Most non-CRF_BF-like recombinant patterns shared at least one common recombination breakpoint with CRF12_BF. The number of transmissions caused by CRF12_BF viruses decreased in a linear way over time, from 69% in the period 1986-1993 to 46% in 2001-2008. In conclusion, the diversity of HIV-1 pol BF1 recombinant structures in Argentina is much more complex than previously described, with at least two CRFs_BF and 26 BF1 unique recombinant forms. For the first time, we provide evidence of a decrease in the proportion of CRF12_BF viruses transmitted from mother-to-child since the start of the epidemic to the present time in Argentina.

Aulicino PC ，Bello G ，Guimaraes ML ，Ruchansky D ，Rocco C ，Mangano A ，Morgado MG ，Sen L ... -  《-》

Characterization of HIV-1 CRF90_BF1 and putative novel CRFs_BF1 in Central West, North and Northeast Brazilian regions.

Reis MNDG ，Bello G ，Guimarães ML ，Stefani MMA ... -  《PLoS One》

Genetic characterization of HIV-1 BC recombinants and evolutionary history of the CRF31_BC in Southern Brazil.

Passaes CP ，Bello G ，Lorete RS ，Matos Almeida SE ，Junqueira DM ，Veloso VG ，Morgado MG ，Guimarães ML ... -  《-》

Complex patterns of the HIV-1 epidemic in Kuala Lumpur, Malaysia: evidence for expansion of circulating recombinant form CRF33_01B and detection of multiple other recombinants.

Wang B ，Lau KA ，Ong LY ，Shah M ，Steain MC ，Foley B ，Dwyer DE ，Chew CB ，Kamarulzaman A ，Ng KP ，Saksena NK ... -  《VIROLOGY》