Analysis of Near Full-Length Genome Sequences of HIV Type 1 BF Intersubtype Recombinant Viruses from Brazil Reveals Their Independent Origins and Their Lack of Relationship to CRF12_BF

Area de Patogenia Viral, Centro Nacional de Microbiología, Instituto de Salud Carlos III. Ctra. Majadahonda-Pozuelo, Km. 2. 28220 Majadahonda (Madrid), Spain.
AIDS Research and Human Retroviruses (Impact Factor: 2.33). 11/2004; 20(10):1126-33. DOI: 10.1089/aid.2004.20.1126
Source: PubMed


We analyze the recombinant structures and phylogenetic relationships of nine near full-length genome sequences of HIV-1 BF intersubtype recombinant viruses from Brazil, eight of them newly derived. These were obtained by PCR amplification from peripheral blood mononuclear cells (PBMCs) DNA or PBMCs culture supernantant RNA. The recombinants exhibited unique mosaic structures, except two viruses with a single near coincident breakpoint. Comparison with CRF12_BF revealed only two coincident breakpoints in two recombinants. Phylogenetic analyses failed to support a common ancestry of Brazilian recombinants or their relationship to CRF12_BF, which widely circulates in Argentina. Intersubtype breakpoint distribution along the genome was uneven, with the highest mean frequency in the polymerase domain of reverse transcriptase, and the lowest in env. These results indicate that HIV-1 BF recombinants from Brazil have independent origins and are unrelated to CRF12_BF, and that intersubtype breakpoints are frequent in pol segments analyzed for drug resistance detection.

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    • "Once more, our findings are in agreement with the distribution of HIV-1 subtypes in the Brazilian epidemic. The Southeast is a region where subtypes B and F co-circulate, in this manner recombinants between these two subtypes can be expected [53], [66]. "
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    ABSTRACT: The present study investigated the prevalence of HIV-1 multiple infections in a population composed by 47 patients under HAART failure and enrolled at the National DST/AIDS, Program, Ministry of Health, Brazil.Detection of multiple infections was done using a previously published RFLP assay for the HIV-1 protease gene, which is able of distinguishing between infections caused by a single or multiple HIV-1 subtypes. Samples with multiple infections were cloned, and sequence data submitted to phylogenetic analysis. We were able to identify 17 HIV-1 multiple infections out of 47 samples. Multiple infections were mostly composed by a mixture of recombinant viruses (94%), with only one case in which protease gene pure subtypes B and F were recovered. This is the first study that reports the prevalence of multiple infections and intersubtype recombinants in a population undergoing HAART in Brazil. Based on the data there was a steep increase of multiple infections after the introduction of the combined antiretroviral therapy in Brazil. Cases of multiple infections may be associated with HIV-1 genetic diversity through recombination allowing for the generation of viruses showing a combination of resistance mutations.
    PLoS ONE 01/2014; 9(1):e84066. DOI:10.1371/journal.pone.0084066 · 3.23 Impact Factor
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    • "New and novel URFs are highly prevalent, and are markedly evident in Africa,43,48,49 South America,50 Cuba,51 China52,53 and Southeast Asia.25,24,27 They can continue to spread in the population, and lead to the emergence of new CRFs. "
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    • "Phylogenetic analysis of previously characterised B/F recombinant HIV-1 sequences showed that all of the sequences of the 13 subjects grouped in the same cluster as B/F recombinant sequences of various South American origins, and showed a close relationship with South American CRF12_BF [Foglieni et al., 2010]. Two recently described BF URFs from Luxemburg and Brazil (accession numbers EU170145 and AY455780 [Thomson et al., 2004]) were the closest to this strain. All of the sequences have been deposited in GenBank under accession numbers HQ834729-HQ834742. "
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