High HIV-1 genetic diversity in Southern Brazil: detection of three South-American CRFs
J. Silveira1, L.R. Goes2, C.P. Muniz2, A.F. Santos2, A.M. Martínez1, U. Tupinambás3, D. Greco3, M.A. Soares2,4
1Fundação Universitaria do Rio Grande, Rio Grande, Brazil, 2Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil, 3Universidade Federal de Minas Gerais, Belo Horizonte, Brazil, 4Instituto Nacional do Câncer, Rio de Janeiro, Brazil
Background: In Brazil, HIV-1 subtypes B and F1 prevail in the AIDS epidemics. Subtype C has been later introduced in the southern region, where it is reported to grow in prevalence over time. Here we analyzed the HIV-1 diversity in the region, looking for new CRFs described in country.
Methods: One hundred and seventy-three patients recently diagnosed for HIV-1 infection (2007-8) at the University Hospital of Rio Grande had their viral RNA isolated from plasma and retrotranscribed. Nested PCR were conducted to amplify genomic regions corresponding to PR, RT, CON and RNH. Products were sequenced and subtyped by phylogenetic analysis. Recombination analyses were conducted with Simplot. Fragments suggestive of CRF were submitted to specific phylogenetic analyses for confirmation.
Results: From 173 isolates amplified and sequenced, 93 (53.8%) were of subtype C, while 44 (25.4%) were of subtype B. Interestingly, we detected a high proportion of mosaic genomes (17.9%). Twenty-four of these were unique recombinant forms (URF): 21 B/C, 2 B/F1 and 1 C/F1. The remaining 4% grouped with known CRFs: 0.6% with CRF31_BC, 0.6% with CRF28/29_BF and 2.9% with CRF12_BF. Of 5 sequences that grouped with CRF12_BF, bootscanning analysis showed that all represented CRF12-derived URF: 3 URF_12C and 2 URF_12B.
Conclusions: Southern Brazil presented a high HIV-1 genetic diversity, where subtype C is still the predominant form. The presence of CRF28/29_BF, originated in Southeastern Brazil, and of CRF12_BF, present in Argentina and Uruguay, shows a continuous change in the region's HIV epidemic influenced by neighboring areas. The introduction of CRF12_BF, although described in Brazil for the first time, already allowed the generation and establishment of a URF_12C virus.
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