The HIV-1 epidemic in Bolivia is dominated by subtype B and CRF12_BF "family" strains

<p>Abstract</p> <p>Background</p> <p>Molecular epidemiological studies of HIV-1 in South America have revealed the occurrence of subtypes B, F1 and BF1 recombinants. Even so, little information concerning the HIV-1 molecular epidemiology in Bolivia is available. In this study we performed phylogenetic analyses from samples collected in Bolivia at two different points in time over a 10 year span. We analyzed these samples to estimate the trends in the HIV subtype and recombinant forms over time.</p> <p>Materials and methods</p> <p>Fifty one HIV-1 positive samples were collected in Bolivia over two distinct periods (1996 and 2005). These samples were genetically characterized based on partial <it>pol protease/reverse transcriptase (pr/rt) </it>and <it>env </it>regions. Alignment and neighbor-joining (NJ) phylogenetic analyses were established from partial <it>env </it>(n = 37) and all <it>pol </it>sequences using Mega 4. The remaining 14 <it>env </it>sequences from 1996 were previously characterized based on HMA-<it>env </it>(Heteroduplex mobility assay). The Simplot v.3.5.1 program was used to verify intragenic recombination, and SplitsTree 4.0 was employed to confirm the phylogenetic relationship of the BF1 recombinant samples.</p> <p>Results</p> <p>Phylogenetic analysis of both <it>env </it>and <it>pol </it>regions confirmed the predominance of "pure" subtype B (72.5%) samples circulating in Bolivia and revealed a high prevalence of BF1 genotypes (27.5%). Eleven out of 14 BF1 recombinants displayed a mosaic structure identical or similar to that described for the CRF12_BF variant, one sample was classified as CRF17_BF, and two others were F1<it>pol</it>/B<it>env</it>. No "pure" HIV-1 subtype F1 or B" variant of subtype B was detected in the present study. Of note, samples characterized as CRF12_BF-related were depicted only in 2005.</p> <p>Conclusion</p> <p>HIV-1 genetic diversity in Bolivia is mostly driven by subtype B followed by BF1 recombinant strains from the CRF12_BF "family". No significant temporal changes were detected between the mid-1990s and the mid-2000s for subtype B (76.2% vs 70.0%) or BF1 recombinant (23.8% vs 30.0%) samples from Bolivia.</p